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Progress in Biophysics and Molecular Biology

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https://www.readbyqxmd.com/read/28943341/a-causal-framework-for-integrating-contemporary-and-vedic-holism
#1
REVIEW
John Kineman
Whereas the last Century of science was characterized by epistemological uncertainty; the current Century will likely be characterized by ontological complexity (Gorban and Yablonsky, 2013). Advances in Systems Theory by mathematical biologist Robert Rosen suggest an elegant way forward (Rosen, 2013). "R-theory" (Kineman, 2012) is a synthesis of Rosen's theories explaining complexity and life in terms of a meta-model for 'whole' systems (and their fractions) in terms of "5(th)-order holons". Such holons are Rosen modeling relations relating system-dependent processes with their formative contexts via closed cycles of four archetypal (Aristotelian) causes...
September 21, 2017: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/28941805/foundations-of-anticipatory-logic-in-biology-and-physics
#2
REVIEW
Jesse S Bettinger, Timothy E Eastman
Recent advances in modern physics and biology reveal several scenarios in which top-down effects (Ellis, 2016) and anticipatory systems (Rosen, 1980) indicate processes at work enabling active modeling and inference such that anticipated effects project onto potential causes. We extrapolate a broad landscape of anticipatory systems in the natural sciences extending to computational neuroscience of perception in the capacity of Bayesian inferential models of predictive processing. This line of reasoning also comes with philosophical foundations, which we develop in terms of counterfactual reasoning and possibility space, Whitehead's process thought, and correlations with Eastern wisdom traditions...
September 20, 2017: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/28941804/mir-132-promotes-the-proliferation-invasion-and-migration-of-human-pancreatic-carcinoma-by-inhibition-of-the-tumor-suppressor-gene-pten
#3
REVIEW
Hui Zhang, Aixiang Liu, Xielin Feng, Lang Tian, Wentao Bo, Haiqing Wang, Yong Hu
MicroRNA (miRNAs) emerges as key oncogene or tumor suppressor in a variety of cancers including pancreatic carcinoma. In this study, we detected the role of miR-132 in development and progression of pancreatic cancer and the underlying mechanism. First, the expression of miR-132 in pancreatic carcinoma and adjacent non-cancerous tissues were detected by qRT-PCR. Then, the role of miR-132 in biological function of pancreatic carcinoma cells was investigated. Our results identified that miR-132 was generally upregulated in pancreatic carcinoma, and phosphatase and tensin homolog (PTEN) was generally downregulated...
September 20, 2017: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/28939327/experience-information-as-the-basis-of-mind-evidence-from-human-decision-making
#4
REVIEW
K Sankaran, Alex Hankey
Study of product diversity by companies and corporations led to the discovery of a new statistical distribution, the (1/f) distribution, assessed according to the Herfindahl-Hirschman index. Products of human creative thinking and decision-making seem to obey the index very widely or universally. This article explores examples of its applications in business and economics as evidence for a new scientific conjecture concerning the physiological basis of Mind: that mind functions from critical instabilities in the brain physiology...
September 19, 2017: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/28939326/peircean-cosmogony-s-symbolic-agapistic-self-organization-as-an-example-of-the-influence-of-eastern-philosophy-on-western-thinking
#5
REVIEW
Søren Brier
Charles S. Peirce developed a process philosophy featuring a non-theistic agapistic evolution from nothingness. It is an Eastern inspired alternative to the Western mechanical ontology of classical science also by the American transcendentalists. Advaitism and Buddhism are the two most important Eastern philosophical traditions that encompass scientific knowledge and the idea of spontaneous evolutionary development. This article attempts to show how Peirce's non-mechanical triadic semiotic process theory can embrace the quantum field view better than the mechanical and information views in a theory of the emergence of consciousness...
September 19, 2017: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/28935153/load-dependent-effects-of-apelin-on-murine-cardiomyocytes
#6
Remi Peyronnet, Christian Bollensdorff, Rebecca A Capel, Eva A Rog-Zielinska, Christopher E Woods, David N Charo, Oleg Lookin, Giovanni Fajardo, Michael Ho, Thomas Quertermous, Euan A Ashley, Peter Kohl
The apelin peptide is described as one of the most potent inotropic agents, produced endogenously in a wide range of cells, including cardiomyocytes. Despite positive effects on cardiac contractility in multicellular preparations, as well as indications of cardio-protective actions in several diseases, its effects and mechanisms of action at the cellular level are incompletely understood. Here, we report apelin effects on dynamic mechanical characteristics of single ventricular cardiomyocytes, isolated from mouse models (control, apelin-deficient [Apelin-KO], apelin-receptor KO mouse [APJ-KO]), and rat...
September 18, 2017: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/28935152/i-ching-dyadic-groups-of-binary-numbers-and-the-geno-logic-coding-in-living-bodies
#7
REVIEW
Zhengbing Hu, Sergey V Petoukhov, Elena S Petukhova
The ancient Chinese book I-Ching was written a few thousand years ago. It introduces the system of symbols Yin and Yang (equivalents of 0 and 1). It had a powerful impact on culture, medicine and science of ancient China and several other countries. From the modern standpoint, I-Ching declares the importance of dyadic groups of binary numbers for the Nature. The system of I-Ching is represented by the tables with dyadic groups of 4 bigrams, 8 trigrams and 64 hexagrams, which were declared as fundamental archetypes of the Nature...
September 18, 2017: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/28919131/optogenetic-targeting-of-cardiac-myocytes-and-non-myocytes-tools-challenges-and-utility
#8
Callum M Johnston, Eva A Rog-Zielinska, Eike M Wülfers, Torsten Houwaart, Urszula Siedlecka, Thomas Knöpfel, Peter Kohl, Franziska Schneider-Warme
In optogenetics, light-activated proteins are used to monitor and modulate cellular behaviour with light. Combining genetic targeting of distinct cellular populations with defined patterns of optical stimulation enables one to study specific cell classes in complex biological tissues. In the current study we attempted to investigate the functional relevance of heterocellular electrotonic coupling in cardiac tissue in situ. In order to do that, we used a Cre-Lox approach to express the light-gated cation channel Channelrhodopsin-2 (ChR2) specifically in either cardiac myocytes or non-myocytes...
September 15, 2017: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/28919132/the-east-the-west-and-the-universal-machine
#9
REVIEW
Bruno Marchal
After reviewing the basic of theology of Universal Numbers/Machines, as detailed in (Marchal, 2007), I illustrate how that body of thought might be used to shed some light upon the apparent dichotomy in Eastern/Western spirituality. This paper relies entirely on my previous inter-disciplinary work in mathematical logic, computer science and machine's theology, where "theology" is used here in the sense of Plato: it is the truth, or the "truth-theory" (in the sense of logicians) about a machine that the machine can either deduce from some of its primitive beliefs, or can be intuited in some sense that eventually is made clear through the modal logic of machine self-reference...
September 14, 2017: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/28916330/brains-language-and-the-argumentative-mind-in-western-and-eastern-societies-the-fertile-differences-between-western-eastern-argumentative-traditions
#10
REVIEW
Jordi Vallverdú
The philosophical differences between Western and Eastern philosophy not only derive from general cultural ideas about reality, but as Nisbet writes (2003), are also methodological, ontological, and cognitively driven. Thus, we can see that strategies of thought and theory-generation are constrained and enabled by conceptual levels, and that the existence of differences and within these levels may be pragmatically combined in fruitful ways. At this point, I remark that there is not a single way to connect biology and culture, but at least we need to admit that brains allow the existence of minds and that these create languages, which also organize the world symbolically following a long set of (sometimes interconnected) heuristics...
September 12, 2017: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/28916329/ecological-extension-of-the-theory-of-evolution-by-natural-selection-from-a-perspective-of-western-and-eastern-holistic-philosophy
#11
REVIEW
Toshiyuki Nakajima
Evolution by natural selection requires the following conditions: (1) a particular selective environment, (2) variation of traits in the population; (3) differential survival/reproduction among types of organisms; and (4) heritable traits. However, the traditional (standard) model does not unclearly explain how and why these conditions are generated or determined. What generates a selective environment? What generates new types? How does a certain type replace, or coexist, with others? In this paper, based on the holistic philosophy in Western and Eastern traditions, I focus on the ecosystem as a higher-level system and generator of conditions that induce the evolution of local populations; I also aim to identify the ecosystem processes that generate those conditions...
September 12, 2017: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/28899724/neo-semiotics-introducing-zeroness-into-peircean-semiotics-may-bridge-the-knowable-and-the-unknowable
#12
REVIEW
Sungchul Ji
No abstract text is available yet for this article.
September 9, 2017: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/28887144/sheaf-theoretic-formulation-for-consciousness-and-qualia-and-relationship-to-the-idealism-of-non-dual-philosophies
#13
REVIEW
Menas C Kafatos, Goro C Kato
Questions about the nature of reality, whether Consciousness is the fundamental reality in the universe, and what is Consciousness itself, have no answer in systems that assume an external reality independent of Consciousness. Ultimately, the ontological foundation of such systems is the absolute division of subject and object. We advocate instead what we consider to be an approach that is in agreement with the foundation of quantum reality, which is based on Rāmānuja's version of Vedanta philosophy and non-dual Kashmir Śaivism...
September 5, 2017: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/28887143/mind-life-continuity-a-qualitative-study-of-conscious-experience
#14
REVIEW
Inês Hipólito, Jorge Martins
There are two fundamental models to understanding the phenomenon of natural life. One is the computational model, which is based on the symbolic thinking paradigm. The other is the biological organism model. The common difficulty attributed to these paradigms is that their reductive tools allow the phenomenological aspects of experience to remain hidden behind yes/no responses (behavioral tests), or brain 'pictures' (neuroimaging). Hence, one of the problems regards how to overcome methodological difficulties towards a non-reductive investigation of conscious experience...
September 5, 2017: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/28887142/marriages-of-mathematics-and-physics-a-challenge-for-biology
#15
REVIEW
Arezoo Islami, Giuseppe Longo
The human attempts to access, measure and organize physical phenomena have led to a manifold construction of mathematical and physical spaces. We will survey the evolution of geometries from Euclid to the Algebraic Geometry of the 20th century. The role of Persian/Arabic Algebra in this transition and its Western symbolic development is emphasized. In this relation, we will also discuss changes in the ontological attitudes toward mathematics and its applications. Historically, the encounter of geometric and algebraic perspectives enriched the mathematical practices and their foundations...
September 5, 2017: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/28887141/epilogue-western-science-reductionism-and-eastern-perspectives
#16
EDITORIAL
Gare Arran
No abstract text is available yet for this article.
September 5, 2017: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/28882719/lessons-from-culturally-contrasted-alternative-methods-of-inquiry-and-styles-of-comprehension-for-the-new-foundations-in-the-study-of-life
#17
REVIEW
Jordi Vallverdú, Marcin J Schroeder
Contemporary scientific approaches to Biology are the result of some cultural ideas considered as universal by Western reductionist traditions. The study of the cultural, symbolic and historical approaches to reality and Life provides us important lessons about the necessity of integrating Eastern holistic views into the study of Life. This is both an epistemological and ontological enhancement which provides more powerful and insightful ways to deal with Life and its understanding.
September 5, 2017: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/28870740/an-extended-framework-for-science
#18
REVIEW
Roland Cazalis
We may be at the cusp of a next generation framework for science which can be facilitated by understanding current limitations in the context of a divergence of 'scientific' tradition from the Axial Age (800-200 BCE) to the present. A powerful advance may come from fusing certain elements from Western and Eastern traditions, synthesizing the framework with an apt understanding of the divergence. Key traits will include the ethopoetic nature of the scientist with attention to his/her experience of self. The framework will also 'access' knowledge through a state of mind less encumbered with paradoxes, duality, incompatibility and other aporias...
September 1, 2017: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/28863930/the-role-of-eastern-approaches-in-david-bohm-s-scientific-philosophical-odysseia
#19
REVIEW
Paavo Pylkkänen
No abstract text is available yet for this article.
August 31, 2017: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/28866124/modeling-the-peak-of-emergence-in-systems-design-and-katachi
#20
REVIEW
Beth Cardier, H T Goranson, Niccolo Casas, Patric Lundberg, Alessio Erioli, Ryuji Takaki, Dénes Nagy, Larry D Sanford
It is difficult to model emergence in biological systems using reductionist paradigms. A requirement for computational modeling is that individual entities can be recorded parametrically and related logically, but their transformation into systems cannot be captured this way. The problem stems from an inability to formally represent system-level interactions and implicit influences, such as context, shifts in causal agency or scale, and self-reference. This hampers biological systems modeling and its computational counterpart, indicating a need for new fundamental abstraction frameworks that include system-level characteristics...
August 30, 2017: Progress in Biophysics and Molecular Biology
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