Some resonances between Eastern thought and Integral Biomathics in the framework of the WLIMES formalism for modelling living systems

Forty-two years ago, Capra published “The Tao of Physics” (Capra, 1975). In this book (page 17) he writes: “The exploration of the atomic and subatomic world in the twentieth century has …. necessitated a radical revision of many of our basic concepts” and that, unlike ‘classical’ physics, the sub-atomic and quantum “modern physics” shows resonances with Eastern thoughts and “leads us to a view of the world which is very similar to the views held by mystics of all ages and traditions.“ This article stresses an analogous situation in biology with respect to a new theoretical approach for studying living systems, Integral Biomathics (IB), which also exhibits some resonances with Eastern thought. Stepping on earlier research in cybernetics1 and theoretical biology,2 IB has been developed since 2011 by over 100 scientists from a number of disciplines who have been exploring a substantial set of theoretical frameworks. From that effort, the need for a robust core model utilizing advanced mathematics and computation adequate for understanding the behavior of organisms as dynamic wholes was identified. At this end, the authors of this article have proposed WLIMES (Ehresmann and Simeonov, 2012), a formal theory for modeling living systems integrating both the Memory Evolutive Systems (Ehresmann and Vanbremeersch, 2007) and the Wandering Logic Intelligence (Simeonov, 2002b). Its principles will be recalled here with respect to their resonances to Eastern thought

Nairobi\u27s Housing Crisis: An Analysis of the Kenya Slum Upgrading Programme

Nairobi, Kenya is one of the most volatile urban centers in Africa, suffering from 60% of its population living in crowded and poverty-stricken informal settlements around the periphery of the city. Efforts to upgrade Nairobi\u27s slums have been attempted by the Government of Kenya (GoK) for decades, using different theories and strategies ranging from forced eviction and demolition to the current Sustainable Livelihoods Approach that claims resident participation as its hallmark. A new initiative based on this strategy entitled the Kenya Slum Upgrading Programme (KENSUP), headed in partnership between the GoK & UN-Habitat, is focusing on Kiberia - East Africa\u27s largest slum of over 700,000 residents. Specifically, the KENSUP\u27s starting point is a village of Kiberia called Soweto, which has a population of approximately 60,000 residents and is considered the poorest section of Kiberia informal settlement. This current venture is entitled the Soweto Slum Upgrading Project (SSUP). On paper, it appears to offer a plausible solution. However, upon interviewing Kiberia\u27s residents, key NGO, UN-Habitat, and the GoK, it is clear that there is a lack of coordination, dialog, and cooperation between the stakeholders of this project. This combined with more enduring factors, such as the lack of clear national policies on land tenure and allocation, and Kiberia\u27s dominant political power structure that has strong economic incentives to maintain the status quo, suggest this large-scale slum upgrading project will not be successful, while smaller and more localized self-help efforts provide a brighter alternative

Parallel Transport over Path Spaces

We develop a differential geometric framework for parallel transport over path spaces and a corresponding discrete theory, an integrated version of the continuum theory, using a category-theoretic framework.Comment: 27pp 3fig pdflatex only; v2: rewritten with several clarifications; v3: minor changes, added references. Version to be published, 30p

Patterns and environmental drivers of juvenile sablefish movement in Southeast Alaska

Thesis (M.S.) University of Alaska Fairbanks, 2018Sablefish Anoplopoma fimbria are a long-lived, deep-dwelling groundfish that inhabit the North Pacific Ocean, ranging from northern Mexico to the Gulf of Alaska to Japan, supporting one of Alaska's most valuable commercial fisheries. After decades of heavy fishing, declines in the Sablefish population led to significant fishing restrictions but few strong year classes developed in recent years. Most Sablefish research has focused on the larval, near-surface juvenile, or adult life history stages, but few studies have examined post-settlement juvenile Sablefish in nearshore areas. This study used acoustic telemetry to understand the presence and movement of juvenile Sablefish in a nursery area in Southeast Alaska. Throughout the summer and fall of 2015 and 2016, 40 juvenile Sablefish implanted with acoustic transmitters were monitored using an array of eight fixed receivers in St. John Baptist Bay, Baranof Island, Alaska. We quantified the movement patterns of 28 juvenile Sablefish using displacement from the head of the bay, daily distance traveled, daily duration within the bay, unique movement types among individuals, and movement in relation to environmental variables. From these analyses, we show that juvenile Sablefish exhibit fidelity to the middle-head region of the bay, display relatively high rates of daily movement and residence, demonstrate three distinct movement patterns, and are influenced by environmental variables like water temperature, diel state, moon phase, and day of year. Our results show that juvenile Sablefish exhibit seasonality in movements as they progressively emigrate from the bay throughout the summer and fall. Certain factors were found to increase the likelihood of movement for juvenile Sablefish, perhaps allowing them to remain in suitable environmental conditions. This study fills a gap in our knowledge of Sablefish early life history and reinforces the importance of nursery areas like St. John Baptist Bay for juvenile Sablefish prior to recruitment into commercial fisheries.Alaska Department of Fish and Gam

Mg(2+) dependency of HIV-1 reverse transcription, inhibition by nucleoside analogues and resistance

Metal ions are essential for DNA polymerase and RNase H activities of HIV-1 reverse transcriptase (RT). RT studies are routinely performed at 6–8 mM Mg(2+), despite the fact that the in vivo concentration might be as low as 0.2 mM. We studied the influence of MgCl(2) and ATP, which likely binds a significant fraction of the magnesium pool in vivo, on the DNA polymerase and RNase H activities of HIV-1 RT, its inhibition by nucleoside RT inhibitors (NRTIs) and primer unblocking by AZT-resistant RT. At low Mg(2+) concentration, reverse transcription of a natural template strongly increased despite a dramatically reduced intrinsic polymerase activity under such conditions. Low Mg(2+) concentrations affected the RNA stability and indirectly decreased its degradation by the RNase H activity. The reduced RNA degradation prevented premature dissociation of the template and primer strands that otherwise generated dead-end DNA products. In addition, low Mg(2+) dramatically decreased the incorporation of NRTIs into DNA and increased nucleotide excision by AZT-resistant RT. The latter effect is also most likely owing to the diminished cleavage of the RNA template. Thus, differences in the free Mg(2+) concentration between different cell types or during the cell cycle might strongly affect HIV-1 replication and its inhibition

Constructing towers with skeletons from open Lie algebras and integrability

We provide a given algebraic structure with the structure of an infinitesimal algebraic skeleton. The necessary conditions for integrability of the absolute parallelism of a tower with such a skeleton are dispersive nonlinear models and related conservation laws given in the form of associated linear spectral problems.Comment: misprints corrected, title changed, some remarks adde

WLIMES, The Wandering LIMES: Towards a Theoretical Framework for Wandering Logic Intelligence Memory Evolutive Systems

This paper compares two complementary theories, Simeonov’s Wandering Logic Intelligence and Ehresmann’s & Vanbremeersch’s Memory Evolutive Systems, in view of developing a common framework for the study of multiscale complex systems such as living systems. It begins by a brief summary of WLI and MES, then analyzes their resemblances and differences. Finally, the article provides an outlook for a future research