Computing Bacterial Evolvability Using Individual-Based Models

2011 ◽  
pp. 190-223
Author(s):  
Richard Gergory ◽  
Richard Vlachos ◽  
Ray C. Paton ◽  
John W. Palmer ◽  
Q. H. Wu ◽  
...  
Keyword(s):  
Parallel Machines ◽  
Multiple Time Scales ◽  
Multiple Time ◽  
Bacterial Cells ◽  
Classifier Systems ◽  
Bacterial Evolution ◽  
Fine Grained ◽  
Learning Classifier ◽  
History Of ◽  
The Individual

This chapter describes two approaches to individual-based modelling that are based on bacterial evolution and bacterial ecologies. Some history of the individual-based modelling approach is presented and contrasted to traditional methods. Two related models of bacterial evolution are then discussed in some detail. The first model consists of populations of bacterial cells, each bacterial cell containing a genome and many gene products derived from the genome. The genomes themselves are slowly mutated over time. As a result, this model contains multiple time scales and is very fine-grained. The second model employs a coarser-grained, agent-based architecture designed to explore the evolvability of adaptive behavioural strategies in artificial bacterial ecologies. The organisms in this approach are represented by mutating learning classifier systems. Finally, the subject of computability on parallel machines and clusters is applied to these models, with the aim of making them efficiently scalable to the point of being biologically realistic by containing sufficient numbers of complex individuals.

scholarly journals Individual-Based Modelling of Bacterial Ecologies and Evolution

2004 ◽  
Vol 5 (1) ◽  
pp. 100-104 ◽  
Author(s):  
C. Vlachos ◽  
R. Gregory ◽  
R. C. Paton ◽  
J. R. Saunders ◽  
Q. H. Wu
Keyword(s):  
Computational Models ◽  
Classifier Systems ◽  
Simulation Experiments ◽  
Computational Tools ◽  
Agent Based ◽  
Fine Grained ◽  
Learning Classifier ◽  
Potential Applications ◽  
The Individual ◽  
Behavioural Strategies

This paper presents two approaches to the individual-based modelling of bacterial ecologies and evolution using computational tools. The first approach is a fine-grained model that is based on networks of interactivity between computational objects representing genes and proteins. The second approach is a coarser-grained, agent-based model, which is designed to explore the evolvability of adaptive behavioural strategies in artificial bacteria represented by learning classifier systems. The structure and implementation of these computational models is discussed, and some results from simulation experiments are presented. Finally, the potential applications of the proposed models to the solution of real-world computational problems, and their use in improving our understanding of the mechanisms of evolution, are briefly outlined.

scholarly journals Multiple time-scales and the developmental dynamics of social systems

2012 ◽  
Vol 367 (1597) ◽  
pp. 1802-1810 ◽  
Author(s):  
Jessica C. Flack
Keyword(s):  
Time Scales ◽  
Social Systems ◽  
Coarse Grained ◽  
Multiple Time Scales ◽  
Multiple Time ◽  
Collective Dynamics ◽  
Individual Level ◽  
Levels Of Organization ◽  
The Individual ◽  
Developmental Dynamics

To build a theory of social complexity, we need to understand how aggregate social properties arise from individual interaction rules. Here, I review a body of work on the developmental dynamics of pigtailed macaque social organization and conflict management that provides insight into the mechanistic causes of multi-scale social systems. In this model system coarse-grained, statistical representations of collective dynamics are more predictive of the future state of the system than the constantly in-flux behavioural patterns at the individual level. The data suggest that individuals can perceive and use these representations for strategical decision-making. As an interaction history accumulates the coarse-grained representations consolidate. This constrains individual behaviour and provides the foundations for new levels of organization. The time-scales on which these representations change impact whether the consolidating higher-levels can be modified by individuals and collectively. The time-scales appear to be a function of the ‘coarseness’ of the representations and the character of the collective dynamics over which they are averages. The data suggest that an advantage of multiple timescales is that they allow social systems to balance tradeoffs between predictability and adaptability. I briefly discuss the implications of these findings for cognition, social niche construction and the evolution of new levels of organization in biological systems.

scholarly journals Indo-Aryan – a house divided? Evidence for the east–west Indo-Aryan divide and its significance for the study of northern South Asia

2020 ◽  
Vol 7 (2) ◽  
pp. 235-274
Author(s):  
Jessica K. Ivani ◽  
Netra Paudyal ◽  
John Peterson
Keyword(s):  
South Asia ◽  
Fine Grained ◽  
History Of ◽  
The Individual ◽  
Asian Languages ◽  
And Linguistics ◽  
Central South ◽  
Opening Up ◽  
Degree Of Similarity ◽  
East West

Abstract In this study, we investigate the possible presence of an east–west divide in Indo-Aryan languages suggested in previous literature (Peterson, John. 2017a. Fitting the pieces together – towards a linguistic prehistory of eastern-central South Asia (and beyond). Journal of South Asian Languages and Linguistics 4(2). 211–257.), with the further hypothesis that this divide may be linked to the influence of the Munda languages, spoken in the eastern part of the subcontinent. Working with 217 fine-grained variables on a sample of 27 Indo-Aryan and Munda languages, we test the presence of a geographical divide within Indo-Aryan using computational methods such as cluster analysis in combination with visual statistical inference. Our results confirm the presence of a geographical divide for the whole dataset and most of the individual features. We then proceed to compute the degree of similarity between the Indo-Aryan languages and Munda, using a Bayesian alternative to a t-test. The results for most features support the claim that the languages identified in the eastern clusters are indeed more similar to Munda, thereby opening up further research scenarios for the history of this region.

scholarly journals The Development of εὑρίσκω ‘find’ as Evidence towards a Diachronic Solution of the Matching-Problem in Ancient Greek Complementation

2020 ◽  
Vol 15 (2) ◽  
pp. 191-207
Author(s):  
Ezra La Roi ◽  
Keyword(s):  
Semantic Role ◽  
Ancient Greek ◽  
Matching Problem ◽  
Bottom Up ◽  
Fine Grained ◽  
History Of ◽  
The Subject ◽  
The Individual ◽  
Predicate Type

This paper traces the semantic and constructional development of the complement-taking verb εὑρίσκω ‘find’ from Homeric Greek to Post-Classical Greek. First, the paper details the semantic development of εὑρίσκω using characteristics such as predicate type, semantic role of the subject and factivity. Subsequently, explanations are offered for the constructional development of εὑρίσκω, using insights from grammaticalization research such as reanalysis and analogy. In contrast to previous studies on Ancient Greek complementation which support the idea of a systematic Classical Greek opposition of factive participial versus non-factive infinitival complementation, this paper shows how bridging contexts of mental judgment εὑρίσκω with a participial complement do not follow this opposition as they are non-factive and changed their meaning (with reanalysis) before changing their complementation structure (through analogy). Also, by extending our view to the individual history of other cognitive predicates (ἐπίσταμαι, γιγνώσκω and οἶδα) the author showsthat other cognitive predicates undergo similar developments from factive+object to factive+ ACP to non-factive+ACI, although their individual histories are still in need of a systematic diachronic account. Thus, complementation patterns per period could be analysed in a more fine-grained way by analysing complementation patterns bottom-up from the semantic and constructional evolutions of individual predicates. Also, the findings from this paper provide evidence towards a diachronic solution of the so-called matching-problem: diachronically related semantic and constructional stages strongly motivate the choice of a specific complementation structure but absolute factivity oppositions in Classical Greek complementation are rather strong tendencies.

Investigating the Relationship Between Self-Esteem and Stigma Among Young Adults With History of Suicide Attempts

Crisis ◽  
2016 ◽  
Vol 37 (4) ◽  
pp. 265-270 ◽  
Author(s):  
Meshan Lehmann ◽  
Matthew R. Hilimire ◽  
Lawrence H. Yang ◽  
Bruce G. Link ◽  
Jordan E. DeVylder
Keyword(s):  
Young Adults ◽  
Suicide Attempts ◽  
Self Esteem ◽  
High Risk Population ◽  
High Functioning ◽  
People With Mental Illness ◽  
History Of ◽  
The Individual ◽  
The Impact ◽  
The Relationship

Abstract. Background: Self-esteem is a major contributor to risk for repeated suicide attempts. Prior research has shown that awareness of stigma is associated with reduced self-esteem among people with mental illness. No prior studies have examined the association between self-esteem and stereotype awareness among individuals with past suicide attempts. Aims: To understand the relationship between stereotype awareness and self-esteem among young adults who have and have not attempted suicide. Method: Computerized surveys were administered to college students (N = 637). Linear regression analyses were used to test associations between self-esteem and stereotype awareness, attempt history, and their interaction. Results: There was a significant stereotype awareness by attempt interaction (β = –.74, p = .006) in the regression analysis. The interaction was explained by a stronger negative association between stereotype awareness and self-esteem among individuals with past suicide attempts (β = –.50, p = .013) compared with those without attempts (β = –.09, p = .037). Conclusion: Stigma is associated with lower self-esteem within this high-functioning sample of young adults with histories of suicide attempts. Alleviating the impact of stigma at the individual (clinical) or community (public health) levels may improve self-esteem among this high-risk population, which could potentially influence subsequent suicide risk.

Victorian Pain

2017 ◽  
Author(s):  
Rachel Ablow
Keyword(s):  
Nineteenth Century ◽  
Victorian Literature ◽  
Social Life ◽  
Charles Darwin ◽  
Harriet Martineau ◽  
The Status ◽  
History Of ◽  
The Individual ◽  
Natural Philosophers ◽  
First Time

The nineteenth century introduced developments in science and medicine that made the eradication of pain conceivable for the first time. This new understanding of pain brought with it a complex set of moral and philosophical dilemmas. If pain serves no obvious purpose, how do we reconcile its existence with a well-ordered universe? Examining how writers of the day engaged with such questions, this book offers a compelling new literary and philosophical history of modern pain. The book provides close readings of novelists Charlotte Brontë and Thomas Hardy and political and natural philosophers John Stuart Mill, Harriet Martineau, and Charles Darwin, as well as a variety of medical, scientific, and popular writers of the Victorian age. The book explores how discussions of pain served as investigations into the status of persons and the nature and parameters of social life. No longer conceivable as divine trial or punishment, pain in the nineteenth century came to seem instead like a historical accident suggesting little or nothing about the individual who suffers. A landmark study of Victorian literature and the history of pain, the book shows how these writers came to see pain as a social as well as a personal problem. Rather than simply self-evident to the sufferer and unknowable to anyone else, pain was also understood to be produced between persons—and even, perhaps, by the fictions they read.

Queering Gender Identity Work: A Life History of a Black Transgender Woman

2018 ◽  
Vol 5 (1) ◽  
Author(s):  
Esethu Monakali
Keyword(s):  
Life History ◽  
Gender Identity ◽  
Public Spaces ◽  
Identity Work ◽  
Social Identities ◽  
Gender And Sexuality ◽  
Ongoing Effort ◽  
History Of ◽  
The Individual

This article offers an analysis of the identity work of a black transgender woman through life history research. Identity work pertains to the ongoing effort of authoring oneself and positions the individual as the agent; not a passive recipient of identity scripts. The findings draw from three life history interviews. Using thematic analysis, the following themes emerge: institutionalisation of gender norms; gender and sexuality unintelligibility; transitioning and passing; and lastly, gender expression and public spaces. The discussion follows from a poststructuralist conception of identity, which frames identity as fluid and as being continually established. The study contends that identity work is a complex and fragmented process, which is shaped by other social identities. To that end, the study also acknowledges the role of collective agency in shaping gender identity.

AN APPRAISAL OF SOURCE MATERIAL FOR THE STUDY OF TARGUM MINOR PROPHETS

2017 ◽  
Vol 24 (2) ◽  
pp. 451-469
Author(s):  
Gudrun Lier ◽  
Anna Fransina Van Zyl
Keyword(s):  
Source Material ◽  
Bible Translations ◽  
Integrated Research ◽  
Translation Techniques ◽  
Former Prophets ◽  
History Of ◽  
The Individual ◽  
History Of Biblical Interpretation ◽  
Work Done ◽  
Minor Prophets

The study of Aramaic Bible translations (Targumim) continues to be a valuable source of information, not only for uncovering the history of biblical interpretation but also for providing insights for the study of linguistics and translation techniques. In comparison with work done on the Pentateuchal Targumim and Targum Former Prophets, research on the individual books of Targum Minor Prophets has been scant. By providing an overview of selected source material this review seeks (i) to provide incentives for more focussed studies in the field of Targum Minor Prophets and (ii) to motivate new integrated research approaches which are now made possible with the assistance of highly developed software programmes.

Distribution, systematics and nomenclature of the three taxa of Common Stonechats (Aves, Passeriformes, Muscicapidae, Saxicola) that breed in the Caucasian region

2020 ◽  
Vol 29 (1) ◽  
pp. 33-57
Author(s):  
V.M. Loskot ◽  
G.B. Bakhtadze
Keyword(s):  
Geographic Distribution ◽  
Habitat Preferences ◽  
Junior Synonym ◽  
Type Locality ◽  
Diagnostic Features ◽  
Western Turkey ◽  
Geographical Variations ◽  
History Of ◽  
The Individual ◽  
North Western

Geographic distribution and habitat preferences of Saxicola rubicola rubicola (Linnaeus, 1766), S. maurus variegatus (S.G. Gmelin, 1774), and S. m. armenicus (Stegman, 1935) inhabiting the Caucasian Isthmus and adjacent areas are described in detail. We examined the individual, sexual, age, seasonal and geographical variations of seven main diagnostic features of both plumage and morphometrics (exactly, the length of wing and tail) using 381 skin specimens. Substantially improved diagnoses of S. m. variegatus and S. m. armenicus are provided. After a thorough examination of the materials and history of the expedition of Samuel Gmelin in 1768–1774, and his description of Parus variegatus, it was concluded that the type locality of this taxon was the vicinity of Shamakhi in Azerbaijan not Enzeli in North-Western Turkey. It is also shown the fallacy of the recently proposed attribution of the holotype of the northern subspecies S. m. variegatus to the southern taxon S. m. armenicus and synonymisation of these names, as well as the replacement of the name S. m. variegatus by its junior synonym S. m. hemrichii Ehrenberg, 1833 for the northern subspecies.

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