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Using Multilevel Temporal Factorisation to Analyse Structure and Dynamics for Higher-Order Adaptive and Evolutionary Processes

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Abstract

To model the dynamics of biological and mental processes of realistic agents as dynamical systems, the structure of the physical or physiological makeup of the agent is an important factor. This paper provides a conceptual and formal analysis based on multilevel temporal factorisation where the structure, dynamics, and adaptivity of these agent processes are distinguished conceptually in a transparent way. Moreover, the multilevel temporal factorisation analysis shows the interplay of these three aspects and how that can be modeled as an adaptive dynamical system represented in a canonical network format. In this way, an agent of any order of adaptivity can be modeled according to a tower of control levels where each level models control over the level below. This is illustrated by different case studies for higher-order adaptive agent processes. One of these case studies concerns a fifth-order adaptive agent model that illustrates how due to bad environmental influences, epigenetic effects on gene expression can lead to mental disorders.

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DNA methylation has been an important area of research in the study of molecular mechanism to psychiatric disorders. Recent evidence has suggested that abnormalities in global methylation, methylation of genes, and pathways could play a role in the etiology of many forms of mental illness. In this article, we review the mechanisms of DNA methylation, including the genetic and environmental factors affecting methylation changes. We report and discuss major findings regarding DNA methylation in psychiatric patients, both within the context of global methylation studies and gene-specific methylation studies. Finally, we discuss issues surrounding data quality improvement, the limitations of current methylation analysis methods, and the possibility of using DNA methylation-based treatment for psychiatric disorders in the future.
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Training rats in a particularly difficult olfactory discrimination task initiates a period of accelerated learning of other odors, manifested as a dramatic increase in the rats' capacity to acquire memories for new odors once they have learned the first discrimination task, implying that rule learning has taken place. At the cellular level, pyramidal neurons in the piriform cortex, hippocampus and bsolateral amygdala of olfactory-discrimination trained rats show enhanced intrinsic neuronal excitability that lasts for several days after rule learning. Such enhanced intrinsic excitability is mediated by long-term reduction in the post-burst after-hyperpolarization (AHP) which is generated by repetitive spike firing, and is maintained by persistent activation of key second messenger systems. Much like late-LTP, the induction of long-term modulation of intrinsic excitability is protein synthesis dependent. Learning-induced modulation of intrinsic excitability can be bi-directional, pending of the valance of the outcome of the learned task. In this review we describe the physiological and molecular mechanisms underlying the rule learning-induced long-term enhancement in neuronal excitability and discuss the functional significance of such a wide spread modulation of the neurons' ability to sustain repetitive spike generation.
Book
A neuroscientific perspective on the mind–body problem that focuses on how the brain actually accomplishes mental causation. The issues of mental causation, consciousness, and free will have vexed philosophers since Plato. In this book, Peter Tse examines these unresolved issues from a neuroscientific perspective. In contrast with philosophers who use logic rather than data to argue whether mental causation or consciousness can exist given unproven first assumptions, Tse proposes that we instead listen to what neurons have to say. Tse draws on exciting recent neuroscientific data concerning how informational causation is realized in physical causation at the level of NMDA receptors, synapses, dendrites, neurons, and neuronal circuits. He argues that a particular kind of strong free will and “downward” mental causation are realized in rapid synaptic plasticity. Such informational causation cannot change the physical basis of information realized in the present, but it can change the physical basis of information that may be realized in the immediate future. This gets around the standard argument against free will centered on the impossibility of self-causation. Tse explores the ways that mental causation and qualia might be realized in this kind of neuronal and associated information-processing architecture, and considers the psychological and philosophical implications of having such an architecture realized in our brains.
Article
The 20 standard amino acids encoded by the Genetic Code were adopted during the RNA World, around 4 billion years ago. This amino acid set could be regarded as a frozen accident, implying that other possible structures could equally well have been chosen to use in proteins. Amino acids were not primarily selected for their ability to support catalysis, since the RNA World already had highly effective cofactors to perform reactions, such as oxidation, reduction and transfer of small molecules. Rather, they were selected to enable the formation of soluble structures with close-packed cores, allowing the presence of ordered binding pockets. Factors to take into account when assessing why a particular amino acid might be used include: its component atoms, functional groups, biosynthetic cost, use in a protein core or on the surface, solubility and stability. Applying these criteria to the 20 standard amino acids, and considering some other simple alternatives that are not used, we find that there are excellent reasons for the selection of every amino acid. Rather than being a frozen accident, the set of amino acids selected appears to be near ideal. This article is protected by copyright. All rights reserved.
Article
Chimpanzees, monkeys, and human subjects were required to respond to a series of delayed reaction situations. In each situation there was a pair of similar receptacles, in the right or left of which the subject had observed food being placed. In some experiments the receptacles were arranged, one pair each, in a number of rooms. In other experiments they were arranged in one room in the form of a circle, the animal being located in the center. The animal, after a given period of delay, was required to obtain the stimulus objects (food) from the appropriate containers, either in the order in which they were placed in one of the various pairs or in broken or reverse order. "With one pair of containers in each of ten rooms the two chimpanzee subjects chose with 88 and 92 per cent accuracy. In the same problem, but with five pairs of containers in five rooms, the monkey subjects made scores of 78 and 80 per cent correct choices. When the pairs of containers were placed about a circle in one room the percentages of correct choices were:[Table omitted]Though the monkey subjects appeared equally eager and attentive, they were far less capable of retaining the memory cues from a long series of situations. In part this limited capacity seemed to be the result of their greater distractability." There was no improvement with practice, hence "the experiment measures native memory capacity." Adult human subjects did not surpass the chimpanzees on the initial 16-pair test. Chimpanzees could respond correctly to a three-container situation after a week's delay. The writer concludes that "the animal subjects respond on the basis of cues of various sorts and from various sources, but that of these, positional cues are the dominant ones." Bibliography. (PsycINFO Database Record (c) 2012 APA, all rights reserved)
Article
In this paper, we review experimental evidence for a novel form of persistent synaptic plasticity we call metaplasticity. Metaplasticity is induced by synaptic or cellular activity, but it is not necessarily expressed as a change in the efficacy of normal synaptic transmission. Instead, it is manifest as a change in the ability to induce subsequent synaptic plasticity, such as long-term potentiation or depression. Thus, metaplasticity is a higher-order form of synaptic plasticity. Metaplasticity might involve alterations in NMDA-receptor function in some cases, but there are many other candidate mechanisms. The induction of metaplasticity complicates the interpretation of many commonly studied aspects of synaptic plasticity, such as saturation and biochemical correlates.
Article
Comparative genomics, using computational and experimental methods, enables the identification of a minimal set of genes that is necessary and sufficient for sustaining a functional cell. For most essential cellular functions, two or more unrelated or distantly related proteins have evolved; only about 60 proteins, primarily those involved in translation, are common to all cellular life. The reconstruction of ancestral life-forms is based on the principle of evolutionary parsimony, but the size and composition of the reconstructed ancestral gene-repertoires depend on relative rates of gene loss and horizontal gene-transfer. The present estimate suggests a simple last universal common ancestor with only 500-600 genes.
The Organisation of Behavior
  • D Hebb
Hebb, D.: The Organisation of Behavior. JohnWiley and Sons (1949)
Philosophical Essays on Probabilities
  • P S Laplace
Laplace, P.S.: Philosophical Essays on Probabilities. Springer, New York (1995). Translated by A.I. Dale from the 5th French edition of 1825 (1825)