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Hierarchy and feedback in the evolution of the Escherichia coli transcription network

M. Cosentino Lagomarsino, P. Jona, B. Bassetti, H. Isambert
2007 Proceedings of the National Academy of Sciences of the United States of America  
This requires a divergent coevolution of the transcription factor DNA-binding sites and their respective DNA cis-regulatory regions.  ...  The E.coli transcription network has an essentially feedforward structure, with, however, abundant feedback at the level of self-regulations.  ...  Note, in particular, that it correctly recovers the actual number of hierarchical layers for tree-like directed graphs (overlooking possible self-regulatory links as in the case of Shen-Orr dataset).  ... 
doi:10.1073/pnas.0609023104 pmid:17372223 pmcid:PMC1838485 fatcat:fe7mnhq46rff5jtmcgar6nr36q

Coevolution of information processing and topology in hierarchical adaptive random Boolean networks

Piotr J. Górski, Agnieszka Czaplicka, Janusz A. Hołyst
2016 European Physical Journal B : Condensed Matter Physics  
Random Boolean networks (RBNs) are frequently employed for modelling complex systems driven by information processing, e.g. for gene regulatory networks (GRNs).  ...  Here we propose a hierarchical adaptive RBN (HARBN) as a system consisting of distinct adaptive RBNs - subnetworks - connected by a set of permanent interlinks.  ...  Our algorithm for the coevolution of hierarchical RBNs is as follows: 1.  ... 
doi:10.1140/epjb/e2015-60530-6 fatcat:ma6ts7tbpvdzrcj7eovyquwte4

Evolution: Spatial Scaling of Microbial Interactions

Rachel J. Whitaker
2009 Current Biology  
Antagonistic interactions and non-self recognition are likely to promote microbial diversity in local populations. Rachel J.  ...  Local intra-and inter-species interactions create a mosaic landscape that can perpetuate coevolution and cause microbes to diversify [7, 8] .  ... 
doi:10.1016/j.cub.2009.09.035 pmid:19889374 fatcat:zd4qr7abqjdifi6xflhbxl4ddm

A comparative evolutionary study of transcription networks [article]

A.L. Sellerio, B. Bassetti, H. Isambert, M. Cosentino Lagomarsino
2008 arXiv   pre-print
The study focuses on the global aspects of feedback and hierarchy in transcriptional regulatory pathways.  ...  of all the analyzed transcription networks, our results point to distinct trends between the bacteria, where time constraints in the transcription of downstream genes might be important in shaping the hierarchical  ...  An AR regulates a homologous, non-self-regulatory transcription factor. 2. An AR is regulated by a homologous, non-self-regulatory transcription factor. 3.  ... 
arXiv:0805.2288v1 fatcat:2hymqr226rfe7harkq7t7s4mmi

Evolution in functional complexity of heart rate dynamics: a measure of cardiac allograft adaptability

J. Yasha Kresh, Igor Izrailtyan
1998 American Journal of Physiology. Regulatory Integrative and Comparative Physiology  
Physiol. 275 (Regulatory Integrative Comp. Physiol. 44): R720-R727, 1998.-The capacity of self-organized systems to adapt is embodied in the functional organization of intrinsic control mechanisms.  ...  Evolution in functional complexity of heart rate variability (HRV) was used as measure of the capacity of the transplanted heart to express newly emergent regulatory order.  ...  Overall, body systems independent of hierarchical organization (molecular to multicellular) normally operate such that a number of regulatory modes are active.  ... 
doi:10.1152/ajpregu.1998.275.3.r720 fatcat:nlyd6tn5vnbx3c46ddbj7eqbcq

Informed Governance: Complexity and the Commons

2015 Complexity Governance & Networks  
For Morcol, the work of Ostrom instructs our current work on self-organization in how institutions of collective action -including hierarchical structures -emerge through self-organization and how the  ...  Entropy -Hierarchical Behavior in the Commons "Defining the Entropy of Hierarchical Organizations," by David Chappell and Greg Dewey, seeks to understand the entropy of organizational structure given personnel  ... 
doi:10.7564/14-cgn15 fatcat:mydnul3iarguxnlxc6kaen4dry

Appropriateness and Structure in Organizations: Secondary Socialization Through Dynamics of Advice Networks and Weak Culture [chapter]

Emmanuel Lazega
2014 Research in the Sociology of Organizations  
This approach helps explore the coevolution of members' relative position in structure and normative choices in their organization.  ...  In this case, coevolution is facilitated by an endogenous process of centralizationÀdecentralizationÀ recentralization of advice networks over time, and by use of a procedural "weak legal culture" that  ...  Thus, to the extent that advice networks are structured by these status games and by their mitigation, they tend to become both hierarchical and cohesive, the hierarchical dimension being often stronger  ... 
doi:10.1108/s0733-558x(2014)0000040019 fatcat:o5vdinw7bjgotkibnnhrbmdbga

Complexity science: Implications for forecasting

Harold A. Linstone
1999 Technological forecasting & social change  
Insightful comparisons among emergent self-organizational patterns are then possible.  ...  For example, the rapid evolution of a global financial system without effective regulatory mechanisms in place raises the specter of financial chaos.  ... 
doi:10.1016/s0040-1625(99)00034-7 fatcat:w6jssdi3wva2hnnhfeql2tahxi

The Coevolution of Transnational Corporations and Institutions

Lundan
2011 Indiana Journal of Global Legal Studies  
Greater reliance on transactions that extend beyond hierarchical control poses a governance challenge.  ...  This requires an ability to set hierarchical incentives in a way that increases employee commitment and maximizes output.  ...  THE COEVOLUTION OF TNCs AND INSTITUTIONS the "obsolescing bargains" struck several decades ago. 86 Here, TNC participation in various kinds of public-private partnerships has the potential to bring about  ... 
doi:10.2979/indjglolegstu.18.2.639 fatcat:zta773a46ffpjhawhd6xhgpxja

Coevolution of Genome Architecture and Social Behavior

Dustin R. Rubenstein, J. Arvid Ågren, Lucia Carbone, Nels C. Elde, Hopi E. Hoekstra, Karen M. Kapheim, Laurent Keller, Corrie S. Moreau, Amy L. Toth, Sam Yeaman, Hans A. Hofmann
2019 Trends in Ecology & Evolution  
We establish guidelines to exploit emerging whole-genome sequences using analytical approaches that examine genome structure and function at different levels (regulatory vs structural variation) from the  ...  The observation of higher levels of imprinting in outcrossing compared with self-fertilizing Arabidopsis species [86] supports this prediction.  ...  As genomic tools and resources become more readily accessible, opportunities to study the coevolution of social behavior and genome architecture abound.  ... 
doi:10.1016/j.tree.2019.04.011 pmid:31130318 fatcat:wji65uy6vzbmnfwtbnma4plhqi

Are we really seeing the big picture? Some reflections on the current debates in evolutionary biology

De-Xing Zhang
2015 Current Zoology  
The ongoing debates in evolutionary biology appear to be self-trapped as such again, worryingly managed only to increase the dimension of chaos.  ...  Appealing and thoughtful it may be as a concept, hierarchical selection needs more than contemplative thinking.  ... 
doi:10.1093/czoolo/61.1.217 fatcat:2fva5n5zgvbipgjhzxxqjoqbia

Strategy of Coevolution Between Biosphere and Society: Ukrainian Dimension

S Rudyshyn
2014 The Advanced Science Journal  
and self-healing.  ...  Biosphere is not entropic and capable of self-organization.  ... 
doi:10.15550/asj.2014.02.090 fatcat:dvojtf35hfhzpimllt6cem25mm

Coevolution of economic behaviour and institutions: towards a theory of institutional change

Jeroen C. J. M. van den Bergh, Sigrid Stagl
2003 Journal of evolutionary economics  
Next, the insights and approaches are integrated into a framework for analysis of institutions based on the notion of coevolution.  ...  Hierarchical processes of learning and changing norms and rules (teleological processes) are often stressed (Stein, 1997) .  ...  Whenever economists recognise that regulatory institutions can change, they tend to apply normative economic policy analysis, which is aimed at proposals as to the way in which institutions should be directed  ... 
doi:10.1007/s00191-003-0158-8 fatcat:s46mvq6m4famtjipuaoebsxtbi

Precision Medicine in Oncology and Immuno-Oncology: Where We Stand and Where We're Headed

Jürgen Scheuenpflug
2017 Biomedicine Hub  
Precision medicine has only been a clinical reality only since the start of the 21st century, spurred on by the coevolution of science and technologies, as well as the increasing medical needs of aging  ...  This article analyzes the recent advances and remaining challenges from a research, medical, and regulatory perspective in the development and introduction of precision medicine in oncology, more precisely  ...  Checkpoints like PD-1 are expressed on regulatory T cells.  ... 
doi:10.1159/000481878 pmid:31988938 pmcid:PMC6945891 fatcat:vy37mo737rfobl6zxhmjemw7oy

Metacognition as a Consequence of Competing Evolutionary Time Scales

Franz Kuchling, Chris Fields, Michael Levin
2022 Entropy  
Furthermore, we show that existing modeling approaches to coadaptation and coevolution—here active inference networks, predator–prey interactions, coupled genetic algorithms, and generative adversarial  ...  ., theoretical self-knowledge [12] .  ...  The architecture shown in Figure 1 is clearly hierarchical.  ... 
doi:10.3390/e24050601 fatcat:2lkuswxylfegzk5tixigua34ii
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