The Tangled Nature model as an evolving quasi-species model

We show that the Tangled Nature model can be interpreted as a general formulation of the quasi-species model by Eigen et al. in a frequency dependent fitness landscape. We present a detailed theoretical derivation of the mutation threshold, consistent with the simulation results, that provides a valuable insight into how the microscopic dynamics of the model determine the observed macroscopic phenomena published previously. The dynamics of the Tangled Nature model is defined on the microevolutionary time scale via reproduction, with heredity, variation, and natural selection. Each organism reproduces with a rate that is linked to the individuals' genetic sequence and depends on the composition of the population in genotype space. Thus the microevolutionary dynamics of the fitness landscape is regulated by, and regulates, the evolution of the species by means of the mutual interactions. At low mutation rate, the macro evolutionary pattern mimics the fossil data: periods of stasis, where the population is concentrated in a network of coexisting species, is interrupted by bursts of activity. As the mutation rate increases, the duration and the frequency of bursts increases. Eventually, when the mutation rate reaches a certain threshold, the population is spread evenly throughout the genotype space showing that natural selection only leads to multiple distinct species if adaptation is allowed time to cause fixation.Comment: Paper submitted to Journal of Physics A. 13 pages, 4 figure

Monolithic ultrasound fingerprint sensor.

This paper presents a 591×438-DPI ultrasonic fingerprint sensor. The sensor is based on a piezoelectric micromachined ultrasonic transducer (PMUT) array that is bonded at wafer-level to complementary metal oxide semiconductor (CMOS) signal processing electronics to produce a pulse-echo ultrasonic imager on a chip. To meet the 500-DPI standard for consumer fingerprint sensors, the PMUT pitch was reduced by approximately a factor of two relative to an earlier design. We conducted a systematic design study of the individual PMUT and array to achieve this scaling while maintaining a high fill-factor. The resulting 110×56-PMUT array, composed of 30×43-μm2 rectangular PMUTs, achieved a 51.7% fill-factor, three times greater than that of the previous design. Together with the custom CMOS ASIC, the sensor achieves 2 mV kPa-1 sensitivity, 15 kPa pressure output, 75 μm lateral resolution, and 150 μm axial resolution in a 4.6 mm×3.2 mm image. To the best of our knowledge, we have demonstrated the first MEMS ultrasonic fingerprint sensor capable of imaging epidermis and sub-surface layer fingerprints

Bio-linguistic transition and Baldwin effect in an evolutionary naming-game model

We examine an evolutionary naming-game model where communicating agents are equipped with an evolutionarily selected learning ability. Such a coupling of biological and linguistic ingredients results in an abrupt transition: upon a small change of a model control parameter a poorly communicating group of linguistically unskilled agents transforms into almost perfectly communicating group with large learning abilities. When learning ability is kept fixed, the transition appears to be continuous. Genetic imprinting of the learning abilities proceeds via Baldwin effect: initially unskilled communicating agents learn a language and that creates a niche in which there is an evolutionary pressure for the increase of learning ability.Our model suggests that when linguistic (or cultural) processes became intensive enough, a transition took place where both linguistic performance and biological endowment of our species experienced an abrupt change that perhaps triggered the rapid expansion of human civilization.Comment: 7 pages, minor changes, accepted in Int.J.Mod.Phys.C, proceedings of Max Born Symp. Wroclaw (Poland), Sept. 2007. Java applet is available at http://spin.amu.edu.pl/~lipowski/biolin.html or http://www.amu.edu.pl/~lipowski/biolin.htm

Revisiting Waiting Times in DNA evolution

Transcription factors are short stretches of DNA (or $k$-mers) mainly located in promoters sequences that enhance or repress gene expression. With respect to an initial distribution of letters on the DNA alphabet, Behrens and Vingron consider a random sequence of length $n$ that does not contain a given $k$-mer or word of size $k$. Under an evolution model of the DNA, they compute the probability $\mathfrak{p}_n$ that this $k$-mer appears after a unit time of 20 years. They prove that the waiting time for the first apparition of the $k$-mer is well approximated by $T_n=1/\mathfrak{p}_n$. Their work relies on the simplifying assumption that the $k$-mer is not self-overlapping. They observe in particular that the waiting time is mostly driven by the initial distribution of letters. Behrens et al. use an approach by automata that relaxes the assumption related to words overlaps. Their numerical evaluations confirms the validity of Behrens and Vingron approach for non self-overlapping words, but provides up to 44% corrections for highly self-overlapping words such as $\mathtt{AAAAA}$. We devised an approach of the problem by clump analysis and generating functions; this approach leads to prove a quasi-linear behaviour of $\mathfrak{p}_n$ for a large range of values of $n$, an important result for DNA evolution. We present here this clump analysis, first by language decomposition, and next by an automaton construction; finally, we describe an equivalent approach by construction of Markov automata.Comment: 19 pages, 3 Figures, 2 Table

Genetic learning as an explanation of stylized facts of foreign exchange markets

This paper revisits the Kareken-Wallace model of exchange rate formation in a two-country overlapping generations world. Following the seminal paper by Arifovic (Journal of Political Economy, 104, 1996, 510-541) we investigate a dynamic version of the model in which agents' decision rules are updated using genetic algorithms. Our main interest is in whether the equilibrium dynamics resulting from this learning process helps to explain the main stylized facts of free-floating exchange rates (unit roots in levels together with fat tails in returns and volatility clustering). Our time series analysis of simulated data indicates that for particular parameterizations, the characteristics of the exchange rate dynamics are, in fact, very similar to those of empirical data. The similarity appears to be quite insensitive with respect to some of the ingredients of the GA algorithm (i.e. utilitybased versus rank-based or tournament selection, binary or real coding). However, appearance or not of realistic time series characteristics depends crucially on the mutation probability (which should be low) and the number of agents (not more than about 1000). With a larger population, this collective learning dynamics looses its realistic appearance and instead exhibits regular periodic oscillations of the agents' choice variables. -- Dieses Papier betrachtet das Kareken-Wallace-Modell für die Wechselkursbildung in einer Welt mit 2 Ländern und sich überlappenden Generationen. In der Nachfolge des zukunftsweisenden Papiers von Arifovic (1996) untersuchen wir eine dynamische Version des Modells bei dem die Entscheidungsregeln mithilfe genetischer Algorithmen jeweils aktualisiert werden. Unser Hauptinteresse geht dahin, herauszufinden, ob die Gleichgewichtsdynamik, die aus diesem Lernprozess resultiert, dabei helfen kann, die wichtigsten stilisierten Fakten von flexiblen Wechselkursen zu erklären (Einheitswurzeln bei den Niveaus mit dicken Enden der Ertragsverteilung und Klumpenbildung bei den Volatilitäten). Unsere Analyse simulierter Daten weist darauf hin, dass für bestimmte Parametrisierungen der Charakter der Wechselkursdynamik tatsächlich dem von empirischen Daten sehr ähnlich ist. Die Ähnlichkeit scheint sehr wenig von speziellen Eigenschaften des gewählten GA-Algorithmus abzuhängen (z. B. nutzenbasiert versus rangbasiert, binäre oder reale Kodierung). Dagegen ist die Mutationswahrscheinlichkeit (die niedrig sein sollte) und die Anzahl der Agenten (die nicht größer als 1000 sein sollte) wichtig. Mit mehr Teilnehmern verliert die kollektive Lerndynamik ihr realistisches Aussehen und es kommt zu regelmäßigen periodischen Schwankungen bei den Variablen, die die Agenten auswählen.Learning,Genetic algorithms,Exchange rate dynamics

Relating high dimensional stochastic complex systems to low-dimensional intermittency

We evaluate the implication and outlook of an unanticipated simplification in the macroscopic behavior of two high-dimensional sto-chastic models: the Replicator Model with Mutations and the Tangled Nature Model (TaNa) of evolutionary ecology. This simplification consists of the apparent display of low-dimensional dynamics in the non-stationary intermittent time evolution of the model on a coarse-grained scale. Evolution on this time scale spans generations of individuals, rather than single reproduction, death or mutation events. While a local one-dimensional map close to a tangent bifurcation can be derived from a mean-field version of the TaNa model, a nonlinear dynamical model consisting of successive tangent bifurcations generates time evolution patterns resembling those of the full TaNa model. To advance the interpretation of this finding, here we consider parallel results on a game-theoretic version of the TaNa model that in discrete time yields a coupled map lattice. This in turn is represented, a la Langevin, by a one-dimensional nonlinear map. Among various kinds of behaviours we obtain intermittent evolution associated with tangent bifurcations. We discuss our results.Comment: arXiv admin note: text overlap with arXiv:1604.0024