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Bickerton D.,University of Hawaii at Manoa | Szathmary E.,Eötvös Loránd University | Szathmary E.,Parmenides Center for the Study of Thinking | Szathmary E.,Institute for Advanced Study
BMC Evolutionary Biology | Year: 2011

The emergence of language and the high degree of cooperation found among humans seems to require more than a straightforward enhancement of primate traits. Some triggering episode unique to human ancestors was likely necessary. Here it is argued that confrontational scavenging was such an episode. Arguments for and against an established confrontational scavenging niche are discussed, as well as the probable effects of such a niche on language and co-operation. Finally, several possible directions for future research are suggested. © 2011 Bickerton and Szathmáry; licensee BioMed Central Ltd.

Zintzaras E.,Institute for Advanced Study | Zintzaras E.,University of Thessaly | Zintzaras E.,Tufts University | Santos M.,Institute for Advanced Study | And 4 more authors.
Journal of Theoretical Biology | Year: 2010

How to design an "evolvable" artificial system capable to increase in complexity? Although Darwin's theory of evolution by natural selection obviously offers a firm foundation, little hope of success seems to be expected from the explanatory adequacy of modern evolutionary theory, which does a good job at explaining what has already happened but remains practically helpless at predicting what will occur. However, the study of the major transitions in evolution clearly suggests that increases in complexity have occurred on those occasions when the conflicting interests between competing individuals were partly subjugated. This immediately raises the issue about "levels of selection" in evolutionary biology, and the idea that multi-level selection scenarios are required for complexity to emerge. After analyzing the dynamical behaviour of competing replicators within compartments, we show here that a proliferation of differentiated catalysts and/or improvement of catalytic efficiency of ribozymes can potentially evolve in properly designed artificial cells where the strong internal competition between the different species of replicators is somewhat prevented (i.e., by choosing them with equal probability). Experimental evolution in these systems will likely stand as beautiful examples of artificial adaptive systems, and will provide new insights to understand possible evolutionary paths to the evolution of metabolic complexity. © 2010 Elsevier Ltd.

Fernando C.,University of Sussex | Fernando C.,UK National Institute for Medical Research | Vasas V.,Autonomous University of Barcelona | Szathmary E.,Institute for Advanced Study | And 3 more authors.
PLoS ONE | Year: 2011

We propose a previously unrecognized kind of informational entity in the brain that is capable of acting as the basis for unlimited hereditary variation in neuronal networks. This unit is a path of activity through a network of neurons, analogous to a path taken through a hidden Markov model. To prove in principle the capabilities of this new kind of informational substrate, we show how a population of paths can be used as the hereditary material for a neuronally implemented genetic algorithm, (the swiss-army knife of black-box optimization techniques) which we have proposed elsewhere could operate at somatic timescales in the brain. We compare this to the same genetic algorithm that uses a standard 'genetic' informational substrate, i.e. non-overlapping discrete genotypes, on a range of optimization problems. A path evolution algorithm (PEA) is defined as any algorithm that implements natural selection of paths in a network substrate. A PEA is a previously unrecognized type of natural selection that is well suited for implementation by biological neuronal networks with structural plasticity. The important similarities and differences between a standard genetic algorithm and a PEA are considered. Whilst most experiments are conducted on an abstract network model, at the conclusion of the paper a slightly more realistic neuronal implementation of a PEA is outlined based on Izhikevich spiking neurons. Finally, experimental predictions are made for the identification of such informational paths in the brain. © 2011 Fernando et al.

Atmanspacher H.,Institute for Frontier Areas of Psychology | Filk T.,Institute for Frontier Areas of Psychology | Filk T.,Albert Ludwigs University of Freiburg | Filk T.,Parmenides Center for the Study of Thinking
Journal of Consciousness Studies | Year: 2012

This contribution addresses major distinctions between the notions of determinism, causation, and prediction, as they are typically used in the sciences. Formally, this can be elegantly achieved by two ingredients: (i) the distinction of ontic and epistemic states of a system, and (ii) temporal symmetry breakings based on the mathematical concept of the affine time group. Key aspects of the theory of deterministically chaotic systems together with historical quotations from Laplace, Maxwell, and Poincaré provide significant illustrations. An important point of various discussions in consciousness studies (notably about 'mental causation' and 'free agency'), the alleged 'causal closure of the physical', will be analyzed on the basis of the affine time group and the breakdown of its symmetries. © Imprint Academic 2011.

Atmanspacher H.,Institute for Frontier Areas of Psychology | Filk T.,Institute for Frontier Areas of Psychology | Filk T.,Albert Ludwigs University of Freiburg | Filk T.,Parmenides Center for the Study of Thinking
Journal of Consciousness Studies | Year: 2012

Temporally non-local measurements - single measurements yielding information about the state of a system at different instances - may provide a way to observe non-classical Behaviour in mental systems. The signature for such Behaviour is a violation of temporal Bell inequalities. We present such inequalities applicable to scenarios with two alternating mental states, such as in the perception of ambiguous figures. We indicate empirical options for testing temporal Bell inequalities, and speculate about possible explanations in case these inequalities are indeed violated. © Imprint Academic 2011.

Filk T.,Albert Ludwigs University of Freiburg | Filk T.,Parmenides Center for the Study of Thinking
Foundations of Physics | Year: 2013

In this article I investigate several possibilities to define the concept of "temporal non-locality" within the standard framework of quantum theory. In particular, I analyze the notions of "temporally non-local states", "temporally non-local events" and "temporally non-local observables". The idea of temporally non-local events is already inherent in the standard formalism of quantum mechanics, and Basil Hiley recently defined an operator in order to measure the degree of such a temporal non-locality. The concept of temporally non-local states enters as soon as "clock-representing states" are introduced in the context of special and general relativity. It is discussed in which way temporally non-local measurements may find an interesting application for experiments which test temporal versions of Bell inequalities. © 2012 Springer Science+Business Media, LLC.

Rodin A.S.,University of Houston | Rodin A.S.,Collegium Budapest Institute for Advanced Study | Szathmary E.,Collegium Budapest Institute for Advanced Study | Szathmary E.,Parmenides Center for the Study of Thinking | And 3 more authors.
Biology Direct | Year: 2011

Background: Synthesis of proteins is based on the genetic code - a nearly universal assignment of codons to amino acids (aas). A major challenge to the understanding of the origins of this assignment is the archetypal "key-lock vs. frozen accident" dilemma. Here we re-examine this dilemma in light of 1) the fundamental veto on "foresight evolution", 2) modular structures of tRNAs and aminoacyl-tRNA synthetases, and 3) the updated library of aa-binding sites in RNA aptamers successfully selected in vitro for eight amino acids.Results: The aa-binding sites of arginine, isoleucine and tyrosine contain both their cognate triplets, anticodons and codons. We have noticed that these cases might be associated with palindrome-dinucleotides. For example, one-base shift to the left brings arginine codons CGN, with CG at 1-2 positions, to the respective anticodons NCG, with CG at 2-3 positions. Formally, the concomitant presence of codons and anticodons is also expected in the reverse situation, with codons containing palindrome-dinucleotides at their 2-3 positions, and anticodons exhibiting them at 1-2 positions. A closer analysis reveals that, surprisingly, RNA binding sites for Arg, Ile and Tyr "prefer" (exactly as in the actual genetic code) the anticodon(2-3)/codon(1-2) tetramers to their anticodon(1-2)/codon(2-3) counterparts, despite the seemingly perfect symmetry of the latter. However, since in vitro selection of aa-specific RNA aptamers apparently had nothing to do with translation, this striking preference provides a new strong support to the notion of the genetic code emerging before translation, in response to catalytic (and possibly other) needs of ancient RNA life. Consistently with the pre-translation origin of the code, we propose here a new model of tRNA origin by the gradual, Fibonacci process-like, elongation of a tRNA molecule from a primordial coding triplet and 5'DCCA3' quadruplet (D is a base-determinator) to the eventual 76 base-long cloverleaf-shaped molecule.Conclusion: Taken together, our findings necessarily imply that primordial tRNAs, tRNA aminoacylating ribozymes, and (later) the translation machinery in general have been co-evolving to ''fit'' the (likely already defined) genetic code, rather than the opposite way around. Coding triplets in this primal pre-translational code were likely similar to the anticodons, with second and third nucleotides being more important than the less specific first one. Later, when the code was expanding in co-evolution with the translation apparatus, the importance of 2-3 nucleotides of coding triplets "transferred" to the 1-2 nucleotides of their complements, thus distinguishing anticodons from codons. This evolutionary primacy of anticodons in genetic coding makes the hypothesis of primal stereo-chemical affinity between amino acids and cognate triplets, the hypothesis of coding coenzyme handles for amino acids, the hypothesis of tRNA-like genomic 3' tags suggesting that tRNAs originated in replication, and the hypothesis of ancient ribozymes-mediated operational code of tRNA aminoacylation not mutually contradicting but rather co-existing in harmony.Reviewers: This article was reviewed by Eugene V. Koonin, Wentao Ma (nominated by Juergen Brosius) and Anthony Poole. © 2011 Rodin et al; licensee BioMed Central Ltd.

Szelag E.,Nencki Institute of Experimental Biology | Szelag E.,University of Social Sciences and Humanities of Warsaw | Szymaszek A.,Nencki Institute of Experimental Biology | Szymaszek A.,University of Social Sciences and Humanities of Warsaw | And 7 more authors.
Restorative Neurology and Neuroscience | Year: 2011

Purposes: The study sets the stage for temporal information processing as a fundamental basis of human cognition and a novel neurorehabilitation method. We focus on auditory perception of temporal order and address the following questions: (1) do subjects' age, gender, hearing status and cognitive functioning influence temporal ordering abilities; (2) are there any differences between Polish and German subjects on these abilities? Methods: 86 Polish and 82 German subjects aged from 20 to 69 years were classified into 5 age groups. Subjects identified the order of two 1-ms clicks presented monaurally in rapid succession. The temporal order threshold (i.e. the minimum temporal gap required to report the stimulus order at 75% correctness) was assessed for each individual. Results: There were no differences between Polish and German subjects on temporal ordering. In both samples, a significant prolongation of temporal-order threshold was observed in subjects older than 60 years of age. Temporal processing was relatively resistant to subjects' hearing status, but it depended on cognitive competence. Thus, it is not chronological age as such but cognitive competence that may explain age-related decreases of temporal acuity. Furthermore, potential effects of age or gender are robust against the language background as no differences were observed between Polish and German subjects. Conclusions: We propose the existence of a neural mechanism underlying the perception of rapid changes in non-verbal acoustic features which constitute a frame for speech perception in many languages. This finding may be important with respect to future applications of temporal training in speech therapy programs designed for patients with receptive language disorders of different etiologies. © 2011 - IOS Press and the authors. All rights reserved.

Boza G.,International Institute For Applied Systems Analysis | Boza G.,Eötvös Loránd University | Boza G.,Parmenides Center for the Study of Thinking | Kun A.,International Institute For Applied Systems Analysis | And 4 more authors.
PLoS Computational Biology | Year: 2012

There is continuing interest in understanding factors that facilitate the evolution and stability of cooperation within and between species. Such interactions will often involve plasticity in investment behavior, in response to the interacting partner's investments. Our aim here is to investigate the evolution and stability of reciprocal investment behavior in interspecific interactions, a key phenomenon strongly supported by experimental observations. In particular, we present a comprehensive analysis of a continuous reciprocal investment game between mutualists, both in well-mixed and spatially structured populations, and we demonstrate a series of novel mechanisms for maintaining interspecific mutualism. We demonstrate that mutualistic partners invariably follow investment cycles, during which mutualism first increases, before both partners eventually reduce their investments to zero, so that these cycles always conclude with full defection. We show that the key mechanism for stabilizing mutualism is phase polymorphism along the investment cycle. Although mutualistic partners perpetually change their strategies, the community-level distribution of investment levels becomes stationary. In spatially structured populations, the maintenance of polymorphism is further facilitated by dynamic mosaic structures, in which mutualistic partners form expanding and collapsing spatial bubbles or clusters. Additionally, we reveal strategy-diversity thresholds, both for well-mixed and spatially structured mutualistic communities, and discuss factors for meeting these thresholds, and thus maintaining mutualism. Our results demonstrate that interspecific mutualism, when considered as plastic investment behavior, can be unstable, and, in agreement with empirical observations, may involve a polymorphism of investment levels, varying both in space and in time. Identifying the mechanisms maintaining such polymorphism, and hence mutualism in natural communities, provides a significant step towards understanding the coevolution and population dynamics of mutualistic interactions. © 2012 Boza et al.

Kun A.,International Institute For Applied Systems Analysis | Kun A.,Eötvös Loránd University | Kun A.,Parmenides Center for the Study of Thinking | Boza G.,International Institute For Applied Systems Analysis | And 3 more authors.
BMC Evolutionary Biology | Year: 2010

Background. Evolution of cooperative behaviour is widely studied in different models where interaction is heterogeneous, although static among individuals. However, in nature individuals can often recognize each other and chose, besides to cooperate or not, to preferentially associate with or to avoid certain individuals. Here we consider a dynamical interaction graph, in contrast to a static one. We propose several rules of rejecting unwanted partners and seeking out new ones, and study the probability of emergence and maintenance of cooperation on these dynamic networks. Results. Our simulations reveal that cooperation can evolve and be stable in the population if we introduce preferential linking, even if defectors can perform it too. The fixation of cooperation has higher probability than that of on static graphs, and this effect is more prevalent at high benefit to cost ratios. We also find an optimal number of partners, for which the fixation probability of cooperation shows a maximum. Conclusions. The ability to recognize, seek out or avoid interaction partners based on the outcome of past interactions has an important effect on the emergence of cooperation. Observations about the number of partners in natural cooperating groups are in concordance with the result of our model. © 2010 Kun et al; licensee BioMed Central Ltd.

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