Solution of the Quasispecies Model for an Arbitrary Gene Network

In this paper, we study the equilibrium behavior of Eigen's quasispecies equations for an arbitrary gene network. We consider a genome consisting of $N$ genes, so that each gene sequence $\sigma$ may be written as $\sigma = \sigma_1 \sigma_2 ... \sigma_N$. We assume a single fitness peak (SFP) model for each gene, so that gene $i$ has some ``master'' sequence $\sigma_{i, 0}$ for which it is functioning. The fitness landscape is then determined by which genes in the genome are functioning, and which are not. The equilibrium behavior of this model may be solved in the limit of infinite sequence length. The central result is that, instead of a single error catastrophe, the model exhibits a series of localization to delocalization transitions, which we term an ``error cascade.'' As the mutation rate is increased, the selective advantage for maintaining functional copies of certain genes in the network disappears, and the population distribution delocalizes over the corresponding sequence spaces. The network goes through a series of such transitions, as more and more genes become inactivated, until eventually delocalization occurs over the entire genome space, resulting in a final error catastrophe. This model provides a criterion for determining the conditions under which certain genes in a genome will lose functionality due to genetic drift. It also provides insight into the response of gene networks to mutagens. In particular, it suggests an approach for determining the relative importance of various genes to the fitness of an organism, in a more accurate manner than the standard ``deletion set'' method. The results in this paper also have implications for mutational robustness and what C.O. Wilke termed ``survival of the flattest.''Comment: 29 pages, 5 figures, to be submitted to Physical Review

A recent appreciation of the singular dynamics at the edge of chaos

We study the dynamics of iterates at the transition to chaos in the logistic map and find that it is constituted by an infinite family of Mori's $q$-phase transitions. Starting from Feigenbaum's $\sigma$ function for the diameters ratio, we determine the atypical weak sensitivity to initial conditions $\xi _{t}$ associated to each $q$-phase transition and find that it obeys the form suggested by the Tsallis statistics. The specific values of the variable $q$ at which the $q$-phase transitions take place are identified with the specific values for the Tsallis entropic index $q$ in the corresponding $\xi_{t}$. We describe too the bifurcation gap induced by external noise and show that its properties exhibit the characteristic elements of glassy dynamics close to vitrification in supercooled liquids, e.g. two-step relaxation, aging and a relationship between relaxation time and entropy.Comment: Proceedings of: Verhulst 200 on Chaos, Brussels 16-18 September 2004, Springer Verlag, in pres

Epidemiology of at-risk alcohol use and associated comorbidities of interest among community-dwelling older adults: a protocol for a systematic review.

There is little epidemiological evidence and knowledge about at-risk alcohol use among community-dwelling older adults and their chronic and acute alcohol-related comorbidities of interest. This systematic review will summarise and examine relevant studies about the epidemiology of at-risk alcohol use and associated comorbidities of interest in this population. We will search the following databases, without language or date restrictions, from inception to 31 August 2019: Embase.com, Medline Ovid SP, Pubmed (NOT medline[sb]), CINAHL EBSCO, PsycINFO Ovid SP, Central-Cochrane Library Wiley and Web of Science (Core Collection). Search strategies will be developed in collaboration with a librarian. We will use predefined search terms for alcoholism, epidemiology, the elderly, living place and comorbidities of interest, as well as terms related to the identification of "measurements", "tools" or "instruments" for measuring harm from alcohol use. At-risk status will be determined by the amount of alcohol consumed and any comorbidities of interest associated with at-risk alcohol use, with the latter being documented separately or using an assessment tool for at-risk drinking. We will also examine the bibliographies of all the relevant articles found and search for unpublished studies. We will consider publications in all languages. No ethical approval is necessary. Results will be presented in national and international conferences on addiction and published in a peer-reviewed journal. CRD42018099965

Coupled Replicator Equations for the Dynamics of Learning in Multiagent Systems

Starting with a group of reinforcement-learning agents we derive coupled replicator equations that describe the dynamics of collective learning in multiagent systems. We show that, although agents model their environment in a self-interested way without sharing knowledge, a game dynamics emerges naturally through environment-mediated interactions. An application to rock-scissors-paper game interactions shows that the collective learning dynamics exhibits a diversity of competitive and cooperative behaviors. These include quasiperiodicity, stable limit cycles, intermittency, and deterministic chaos--behaviors that should be expected in heterogeneous multiagent systems described by the general replicator equations we derive.Comment: 4 pages, 3 figures, http://www.santafe.edu/projects/CompMech/papers/credlmas.html; updated references, corrected typos, changed conten

Kohn Anomalies in Superconductors

I present the detailed behavior of phonon dispersion curves near momenta which span the electronic Fermi sea in a superconductor. I demonstrate that an anomaly, similar to the metallic Kohn anomaly, exists in a superconductor's dispersion curves when the frequency of the phonon spanning the Fermi sea exceeds twice the superconducting energy gap. This anomaly occurs at approximately the same momentum but is {\it stronger} than the normal-state Kohn anomaly. It also survives at finite temperature, unlike the metallic anomaly. Determination of Fermi surface diameters from the location of these anomalies, therefore, may be more successful in the superconducting phase than in the normal state. However, the superconductor's anomaly fades rapidly with increased phonon frequency and becomes unobservable when the phonon frequency greatly exceeds the gap. This constraint makes these anomalies useful only in high-temperature superconductors such as $\rm La_{1.85}Sr_{.15}CuO_4$.Comment: 18 pages (revtex) + 11 figures (upon request), NSF-ITP-93-7

Contemporary Issues of Open Data in Information Systems Research: Considerations and Recommendations

Researchers, governments, and funding agencies are calling on research disciplines to embrace open data—data that anyone can access and use. They have done so based on the premise that research efforts can draw and generate several benefits from open data because it might provide further insight and enable individuals to replicate and extend current knowledge in different contexts. These potential benefits, coupled with a global push towards open data policies, bring open data into the agenda of research disciplines, which includes information systems (IS). In this paper, we respond to these developments as follows. We outline themes in the ongoing discussion around open data in the IS discipline. The themes fall into two clusters: 1) the motivation for open data includes themes of mandated sharing, benefits to the research process, extending the life of research data, and career impact; and 2) the implementation of open data includes themes of governance, socio-technical system, standards, data quality, and ethical considerations. In this paper, we outline the findings from a pre-ICIS 2016 workshop on the topic of open data. The workshop discussion confirmed themes and identified issues that require attention in terms of the approaches that IS researchers currently use. The IS discipline offers a unique knowledge base, tools, and methods that can advance open data across disciplines. Based on our findings, we provide suggestions on how IS researchers can drive the open data conversation. Further, we provide advice for adopting and establishing procedures and guidelines for archiving, evaluating, and using open data

Un système d'acquisition de données pour l'analyse en ligne des photographies de grandes chambres à bulles

Ce travail présente le système d'analyse des clichés de grandes chambres à bulles telles que Gargamelle et BEBC, réalisé au Groupe de Chambre à Bulles à Liquide Lourd à l'aide d'appareils de projection mis en ligne sur ordinateur CDC 1700. Ce travail présente les caractéristiques générales de ces appareils ainsi que celles de l'ordinateur et développe la conception et les fonctions des programmes d'analyse des photographies : prémesures, mesures et gestion des données. L'ensemble du système d'acquisition de données fonctionne dans un contexte de multiprogrammation en temps réel

Contemporary issues of open data in information systems research: considerations and recommendations

Researchers, governments, and funding agencies are calling on research disciplines to embrace open dataâ data that anyone can access and use. They have done so based on the premise that research efforts can draw and generate several benefits from open data because it might provide further insight and enable individuals to replicate and extend current knowledge in different contexts. These potential benefits, coupled with a global push towards open data policies, bring open data into the agenda of research disciplines, which includes information systems (IS). In this paper, we respond to these developments as follows. We outline themes in the ongoing discussion around open data in the IS discipline. The themes fall into two clusters: 1) the motivation for open data includes themes of mandated sharing, benefits to the research process, extending the life of research data, and career impact; and 2) the implementation of open data includes themes of governance, socio-technical system, standards, data quality, and ethical considerations. In this paper, we outline the findings from a pre-ICIS 2016 workshop on the topic of open data. The workshop discussion confirmed themes and identified issues that require attention in terms of the approaches that IS researchers currently use. The IS discipline offers a unique knowledge base, tools, and methods that can advance open data across disciplines. Based on our findings, we provide suggestions on how IS researchers can drive the open data conversation. Further, we provide advice for adopting and establishing procedures and guidelines for archiving, evaluating, and using open data

Reply to editorial and commentaries on Steele, Al-Mufti, Augustyn, Chandrajith, Coghlan, Coulson et al. (2018) "Cause of Cambrian explosion - Terrestrial or cosmic?"

No abstract availabl

Reply to commentary by R Duggleby (2019)

Duggleby (2018) has made a numerical analysis of some aspects of the wide range of phenomena we reviewed in Steele et al. (2018) and asserted " .that panspermia as proposed by Steele et al. (2018) is extremely implausible.” It seems to us that Duggleby has based his viewpoint on a quite narrow and specific model of Panspermia which he supposes to be active in the cosmos. Here we address both his conclusions and his numerical analysis. Our response therefore will be at two levels, his specific analysis and his general conclusions. In the specific section below we show that while Duggleby's numerical analysis appears in part correct it is, in the final analysis, quite irrelevant to Cosmic Panspermia. In the general response which follows we address his unsupported conclusion throughout his critique, namely that … " none of the examples mentioned by Steele et al. (2018) is decisive enough to allow no other explanation.