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Complexity Digest -- Toolkit Containing Root Research Results, Articles, Books, and Software -- Covers Emergence, Self-Organization, and Beyond

Goal: To everyone who wants to quickly achieve and constantly improve a wide and deep overview of important complex systems RESEARCH RESULTS, RESEARCH AND REVIEW PAPERS, METHODS, BOOKS, AND SOFTWARE from all scientific fields should visit this project.

All researchers working in mathematics, physics, across chemistry, toward biology and medicine can gain new and deep insights into the CSs problem-solving here.


CALL FOR IMPORTANT PAPERS, BOOKS, SOFTWARE LINKS

Valuable submissions of important information from the field are welcomed. Send preferentially an RG link and explanation of why you think that the given information should be shared here.

We all, together, through mutual cooperation, can accomplish much more compared to when we work alone. We are here to teach each other.

Methods: Game Theory, Lattice Boltzmann Methods, Entropy, Agent-Based Models , Complex Networks, Cellular Automata, Complex systems, Complexity, Emergence, Self-organization

Date: 11 February 2020

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Jiří Kroc
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K.K. Shah,  S. Tripathi,  I. Tiwari, J. Shrestha, B. Modi, N. Paudel & B.D. Das
AGRICULTURAL SCIENCE AND  TECHNOLOGY, 13:2 (2021) 109-118
DOI: 10.15547/ast.2021.02.019
Abstract.
Global  food production  needs to be increased  in order to feed the world’s growing population  and at the same time, the reliance on  inorganic  fertilizers  and  pesticides  should  be  minimized.  To  accomplish  this  goal,  the  various  beneficial  associations  between  plants  and soil microorganisms should  be explored.  The soil microbes  are bacteria,  actinomycetes,  viruses,  fungi, nematode, and protozoa.  They have an  important  soil  function  that  has  fulfilled  several  useful  tasks  in  the  soil  system.  Microbes  support  biological  nitrogen  fixation  of  different biological  transformations  that support  the  accumulation  and  utilization  of  key  nutrients,  support  root  and  shoot  growth  processes, disease control,  and improve  soil  quality  in  crop cultivation.  Soil  microbes  offer nutrient-dense  nourishment  improved  crop  production  and  recycle  soil solutions.  They  play  an  essential  role  in  decomposing  organic  matter, cycling  nutrients,  and  fertilizing  the  soil.  Besides,  they  improve  plant growth  on various physiological  parameters of plants by a number of mechanisms.  The mechanism involved in growth  promotion includes plant growth regulators, production  of  different  metabolites,  and  conversion  of  atmospheric  nitrogen  into  ammonia  in  direct  and  indirect  ways.  In addition,  soil  microbes  offer  resistance  against  diseases.  This  review  outlines  the  significant  impact  of  soil  microbes  on  sustainable  agricultural growth, the benefits of microbes in maintaining soil health, and  their  interactions.
Bacteria
Bacteria  are so  basic  in structure  that they  are sometimes referred to as bags of enzymes  and/or fertilizer  soluble  bags (Dick, 2009).  In crop processing,  soil bacteria have  a  key role as they  take part in the processes that  provide  soil nutrients (Davison,  1988), boosting  plant growth, e.g.  plant  hormone development,  regulating or inhibiting  plant pathogens, improving  the composition  of the soil  as well as  bioaccumulation and  inorganic microbial leaching.  Nitrogen content (10-30% N, 3 to 10 C:N  ratio) in bacteria is higher than most microbes (Hoorman and Islam, 2010).  Ingham  (2009)  defines  the  four main  functional  groupings  of soil  bacteria  as  decomposers, mutualists,  pathogens,  and lithotrophs.  Each functional  bacteria category plays a role in recycling soil nutrients.
...
Soil  microbes  play  a  significant  role  in the tolerance  to plant  diseases.  They  can  prevent  pathogen  infection  by inducing  plant  systemic  disease  resistance  and by coating root surfaces  to physically  shield  the  plant  from getting infected by pathogens.  Soil microbes  can make  plants  more resistant to an aggressive  disease, thus  opening  new possibility  for sustainable food production (University of  York, 2019).
...
Ecological balance among plants, soil and microbes
Bio-fertilizer  is  also used in organic farming systems, but at present, the option of plant cultivars and microbial inoculants have  little mechanistic  understanding  (Bender et al., 2016). Balanced utilization of organic fertilizers enhances  fertilizer  efficiency  and  physical,  chemical,  or biological soil environment, contributing to an increase in crop production (Tiwari et al., 2021). Plants interact with these soil-inhabiting species in several ways that cover the entire spectrum of ecological possibilities (competitive, exploitative, cooperative,  commensal, and mutual).  Many of the plantbased interactions have been focused in modern sciences on alleviating pathogens such as herbivory and infection, or reducing abiotic stress conditions.  Yaish et al. (2016) established that  microbial metabolism speeds up organic matter decomposition, facilitates  nutrient mineralization, and enables  plant  absorbed  nutrients.  Efflux  of  CO2  from soil stems from  two  distinct  factors  such as  root and microbial  respiration rhizosphere  and  soil  organic  microbial  decomposition. Importantly,  nitrogen-fixing  bacteria  in  the  rhizosphere  may  be used  to  fix  nitrogen  in  order  to  provide  organic  and  inorganic nitrogen to plants  (Dominati  et al., 2010).
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Conclusion
The soil  microbes  are bacteria,  actinomycetes,  viruses, fungi, nematode, and protozoa.  They produce plant growth regulators  and metabolites  that affect  the plant  growth and development.  Soil microbes  are critical  to decomposing  organic residues  and  recycling  soil  nutrients.  They  provide  nutrients  to crops,  enhance  soil  health  and crop  outputs.  Soil  microbes  play a  significant  part  in  the  tolerance  to  plant  diseases.  Considering the environmental damage associated  with use of chemical fertilization,  a research  priority  on optimizing  plant-soil  microbe nutritional  interactions  is  essential  for more sustainable agricultural systems.
 
This is an eyes wide opening review. Thanks go to the authors.
 
Jiří Kroc
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Polar night Energy company
July 5, 2022
Everyone interested about very cheap heating of houses during winter season should read this article. This topic is currently very hot.
Abstract:
Polar Night Energy’s first commercial sand-based high temperature heat storage is now in operation at Vatajankoski power plant area. The heat storage, which has a hundred tons of sand inside, is producing low emission district heating to the city of Kankaanpää in Western Finland. BBC made a story about Polar Night Energy’s heat storage solution.
Link to the full text:
Contact information
Polar Night Energy
Markku Ylönen
Co-Founder & CTO
+358 45 7832 8399
Vatajankoski
Pekka Passi
Managing Director
+358 40 508 6367
The ilustrative video link:
 
Jiří Kroc
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Ashok K. Rathoure
In book: Editors: Dr Ashok K Rathoure, Bioremediation Current Research and Application  Chapter 2, IK International 2017
Background The  rapid  industrial  developments  have  led  to  the  generation  of  huge  quantities  of hazardous  wastes,  which  have  further  aggravated  the  environmental  problems  in the  country  by  depleting  and  polluting  natural  resources.  Therefore,  rational  and sustainable  utilization  of  natural  resources  and  its  protection  from  toxic  releases  is  vital for  sustainable  socio-economic  development  (Chakrabarti  et  al.,  2006).  Hazardous  waste management  is  a  new  concept  for  most  of  the  Asian  countries  including  India.  The  lack of  technical  and  financial  resources,  and  the  regulatory  control  for  the  management  of hazardous  wastes  in  the  past  had  led  to  the  unscientific  disposal  of  hazardous  wastes in  India,  which  posed  serious  risks  to  human,  animal  and  plant  life.  A  huge  quantity of  pollutants  in  the  form  of  domestic  and  industrial  effluents  is  discharged  directly or  indirectly  into  the  water  bodies,  which  has  severe  impacts  on  its  biotic  and  abiotic environment.  During  rain,  surface  water  with  soil,  mud  and  humus  enter  into  the river,  tanks  and  other  water  bodies.  The  soil  is  the  target  of  thousands  of  contaminants that  vary  in  composition  and  in  concentration.  The  contaminants  enter  the  system  as  a result  of  a  wide  range  of  actions,  such  as  intentional  applications,  inadequate  residue disposal,  accidental  wastes  and  inappropriate  use.  Some  human  activities  have  resulted in  the  accumulation  of  metals  in  the  environment.  The  inorganic  minerals  like  sodium, potassium,  calcium,  magnesium  and  heavy  metals  like  iron,  manganese,  lead,  mercury, chromium,  cadmium,  nickel,  cobalt,  beryllium,  copper,  etc.,  when  reach  to  the  river with  water  cause  water  pollution.  The  use  of  various  types  of  pesticides  and  insecticides in  agriculture  also  cause  water  pollution.  The  pathogenic  organisms  of  these  wastes transmit  to  the  water  and  pose  serious  problems  (Batley,  1989;  Garbarino  et  al.,  1995; Jogdand,  1995;  Agarwal,  1998;  Hakeem  and  Bhatnagar,  2010).
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Conclusion:
While  anthropogenic  activities  are  the  major  source  of  heavy  metal  pollution,  natural sources  contribute  significantly  to  the  burden  of  arsenic  and  fluoride.  Apart  from industries,  road  runoff  is  also  an  important  source.  The  toxic  elements  enter  the  body mainly through water, food and air. Cosmetics, dental products, some drugs, particularly Ayurvaid  and  Unani  drugs  also  contribute.  Major  pollutants  are  introduced  into  the aquatic  systems  significantly  as  a  result  of  various  industrial  operations.  The  lack of  technical  and  financial  resources  and  the  regulatory  control  for  the  management of  hazardous  wastes  in  the  past  had  led  to  the  unscientific  disposal  of  hazardous wastes,  which  posed  serious  risks  to  human,  animal  and  plant  life.  A  huge  quantity of  pollutants  in  the  form  of  domestic  and  industrial  effluents  is  discharged  directly  or indirectly  into  the  soil/water  bodies,  which  has  severe  impacts  on  its  biotic  and  abiotic environment.  During  rain,  surface  water  with  soil,  mud  and  humus  enter  into  the  river, tanks  and  other  water  bodies.  The  inorganic  minerals  like  sodium,  potassium,  calcium, magnesium and heavy metals like iron, manganese, lead, mercury, chromium, cadmium, nickel,  cobalt,  copper  etc.,  when  reach  to  the  soil/river  water  caused  pollution.  Heavy metal  contamination  is  becoming  a  great  concern  to  the  environmental  awareness  and government  policies.  Several  heavy  metal  removal  technologies  including  chemical precipitation,  ion  exchange,  reverse  osmosis,  electrodialysis,  ultrafiltration  and phytoremediation  are  commonly  used  in  industries.  However,  these  technologies  are becoming  uneconomical  and  unfavourable  to  remove  heavy  metal  from  contaminated sites  or  wastewater.  With  increasing  environmental  attention  and  legal  constraint  on discharge  effluents,  a  need  of  cost  effective  technology  is  essential.  Therefore,  the  search for  efficient,  eco-friendly  and  cost  effective  remedies  for  wastewater  treatment  has  been initiated.  In  recent  years,  research  attention  has  been  focused  on  biological  method, e.g.,  bioremediation,  is  in  the  process  of  commercialization.  Bioremediation  provides  a technique  for  cleaning  up  pollution  by  enhancing  the  natural  biodegradation  processes. The  bioremediation  is  one  of  the  most  promising  technological  approaches  to  the problem  of  hazardous  waste.  This  process  relies  on  microorganisms,  such  as  bacteria or  fungi  to  transform  hazardous  chemicals  into  less  toxic  or  nontoxic  substances.  Such biological  transformation  is  more  attractive  than  direct  chemical  or  physical  treatment. Microorganisms  directly  degrade  contaminants  rather  than  merely  transferring  them from  one  medium  to  another,  employ  metabolic  degradation  pathways  and  can  be used  in  situ  to  minimize  disturbance  of  the  cleanup  site.  Hence,  microorganisms  can be  effective,  economical  and  non-disruptive  tools  for  eliminating  hazardous  chemicals. There  is  no  doubt  that  bioremediation  is  in  the  process  of  paving  a  way  to  greater pastures.  This  technology  offers  an  efficient  and  cost  effective  way  to  treat  contaminated soil,  waste  and  water.  Its  advantage  generally  outweigh  the  disadvantage,  therefore  may be  used  as  management  tool.
 
Jiří Kroc
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Ashok K Rathoure
IK International Publisher, 2017, pp. 476
ISBN: 978-93-85909-60-3
Abstract
Bioremediation is one of the most promising technological approaches to the problem of hazardous waste, which relies on microorganisms such as bacteria or fungi to transform hazardous chemicals into less toxic or nontoxic substances. Such biological transformation is more attractive than direct chemical or physical treatment. Microorganisms directly degrade contaminants rather than merely transferring them from one medium to another, employ metabolic degradation pathways and can be used in situ to minimize disturbance of the cleanup site. Hence, microorganisms can be effective, economical and non-disruptive tools for eliminating hazardous chemicals. There is no doubt that bioremediation is in the process of paving a way to greater pastures. The book aims to provide relevant theoretical and practical frameworks and the latest empirical research findings in this area, along with case studies. It is written for students, academicians and industry professionals who want to improve their understanding of the strategic role of bioremediation at different levels of the bioremediation research and knowledge, that is, heavy metal pollution, toxicity, remediation methods and strategies to manage the waste in industries, which are a global concern.
 
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T.P. Swarnam, Eaknath B. Chakurkar & A. Velmurugan
Abstract:
Agriculture intensification with modern chemical inputs has resulted in increasing food production but not without adverse impacts on the environment. Therefore alternative farming methods like natural farming (NF) is advocated to minimise the input cost and sustain the soil health. An assessment was carried out based on the data collected from field experiments, published reports and field survey. The results showed that NF has shown significant yield advantages mainly under rainfed, low input agricultural system than conventional / organic farming. Low input, rainfed crops such as finger millet, sorghum and black gram gave comparable yield in NF. Under island condition NF supplemented with organic manures significantly improved coconut yield and soil biological properties. The study also revealed that integration of livestock component and cultivating spices as intercrops, green fodder and green manure crops as live mulch in coconut plantations along with NF practices such as application of jeevamruth and practising of mulching can play a significant role in increasing the productivity of coconut besides improving soil biological activities in the islands. PCA analysis indicated separation and loading of different farming methods in various quadrants of the PCA plots. In NF resource optimization is not achieved whereas intensive and specialized farming are resource degrading and lack stability. Therefore, it is suggested to combine and optimise some of the best practices of NF and organic farming under various farming situations for different crops without compromising crop yield and farmers income.
Abstract jeevamruth Key  words:  farming  types,  crop  yield,  organic  inputs,  jeevamruth,  soil  enzyme  activity,
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This paper is very interesting because it demonstrates the way to grow food without necessity to use chemicals, heavy machinery, and other means of industrial agriculture, which leads to high crop yields and profit without compromising ecosystems!
 
Jiří Kroc
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Gabriela Niemeyer Reissig, Thiago Francisco de Carvalho Oliveira, Ricardo Padilha de Oliveira, Douglas Antônio Posso, André Geremia Parise, Dori Edson Nava & Gustavo Maia Souza
Frontiers in Sustainable Food Systems 5:244 (2021) 657401
DOI: 10.3389/fsufs.2021.657401
Abstract:
The electrical activity of tomato plants subjected to fruit herbivory was investigated. The study aimed to test the hypothesis that tomato fruits transmit long-distance electrical signals to the shoot when subjected to herbivory. For such, time series classification by machine learning techniques and analyses related to the oxidative response were employed. Tomato plants (cv. “Micro-Tom”) were placed into a Faraday’s cage and an electrode pair was inserted in the fruit’s peduncle. Helicoverpa armigera caterpillars were placed on the fruit (either green and ripe) for 24h. The time series were recorded before and after the fruit’s exposure of the caterpillars. The plant material for chemical analyses was collected 24 and 48haftertheendoftheacquisition of electrophysiological data. The time series were analyzed by the following techniques: Fast Fourier Transform (FFT), Wavelet Transform, Power Spectral Density (PSD), and Approximate Entropy. The following features from FFT, PSD, and Wavelet Transform were used for PCA (Principal Component Analysis): average, maximum and minimum value, variance, skewness, and kurtosis. Additionally, these features were used in Machine Learning (ML) analyses for looking for classifiable patterns between tomato plants before and after fruit herbivory. Also, we compared the electrome before and after herbivory in the green and ripe fruits. To evaluate an oxidative response in different organs, hydrogen peroxide, superoxide anion, catalase, ascorbate peroxidase, guaiacol peroxidase, and superoxide dismutase activity were evaluated in fruit and leaves. The results show with 90% of accuracy that the electrome registered in the fruit’s peduncle before herbivory is different from the electrome during predation on the fruits. Interestingly, there was also a sharp difference in the electrome of the green and ripe fruits’ peduncles before, but not during, the herbivory, which demonstrates that the signals generated by the herbivory stand over the others. Biochemical analysis showed that herbivory in the fruit triggered an oxidative response in other parts of the plant. Here, we demonstrate that the fruit perceives biotic stimuli and transmits electrical signals to the shoot of tomato plants. This study raises new possibilities for studies involving electrical signals in signaling and systemic response, as well as for the applicability of ML to classify electrophysiological data and its use in early diagnosis.
Keywords: plant electrophysiology, machine learning, Micro-Tom, Helicoverpa amigera, stress response, antioxidant system
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Discussion:
...
Concluding, the tomato fruit is a plant organ capable of sensing biotic stimuli and transmitting electrical signals to the shoot of tomato plants. Besides, the signaling between fruit and shoot triggered biochemical processes related to biotic stress responses in different leaves and fruits. Finally, we observed that the electromeinthepedunclewasdifferentbetweenmaturegreen and red fruits, indicating that electrical signals might be involved in the ripening process. This study raises new possibilities for studies involving electrical signals in signaling and systemic responses, as well as for the applicability of ML to classify electrophysiological data and its use in early diagnosis. It could contribute to a more sustainable crop and food production.
 
Jiří Kroc
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Prakash Bahadur Chand, Kamal Joshi, Ronika Thapa, Ashish Lamsal & Bijay Chauhan
Tropical Agroecosystems (TAEC) 3(1) (2022) 16-22
DOI: 10.26480/taec.01.2022.16.22
Abstract
Increasing use of agrochemicals, higher cost, and deteriorating ecosystem health have advocated the requirement to vary external input use agriculture towards safe and sustainable organic production. Current research focuses on the factors affecting the adoption of organic farming by selecting farmers of the Darchula District. This study adopted a sampling technique to pick 62 respondents. From the survey, it had been found that there have been mainly subsistence farmers that mean growing agricultural products for his or her own consumption. Most of them don't have food self-sufficiency for a year The findings revealed that the bulk of the households were male headed (79.03%) and literature (76%). Most of the farmers had a mean landholding of about 0.58 ha. Most of the farmers were lacking training on organic farming. The foremost problems of the study area were a scarcity of information about organic farming and government intervention. Most of the farmers are practicing organic farming and that they don't realize this fact. The farmers are able to adopt organic farming in next the five years if the government provides proper training and knowledge about the certification process.
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Conclusion:
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Our study showed that the majority of the respondents about 98.45% did not know about organic farming. Although 98.4% of respondents had never used the chemicals in farming and their products were organic but they had no idea whether it is organic or inorganic. The use of chemical input is negative for the health of people and animals was found major governing for adopting organic farming while government support to organic farming is found least governing factor for adopting organic farming in that area. There is a virtual lack of government support to the organic growers & marketers. The constraints could be seen in three actors of organic production viz; at growers’ level, at marketers level, and government level. Lack of awareness, lack of skill in managing the complex problem in the farmland, lack of sufficient technology to support organic production, no certification, and labeling, poor investment capacity, smallholdings, the less risk-bearing capacity of the organic producers, etc.; are the major problems at producers’ level. 
...
 
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Robert Neil Gerard Miller, Gabriel Sergio Costa Alves & Marie-Anne Van Sluys
Annals of Botany 119: 681–687, 2017
DOI:10.1093/aob/mcw284
Abstract:
Background Plants are constantly exposed to evolving pathogens and pests, with crop losses representing a considerable threat to global food security. As pathogen evolution can overcome disease resistance that is conferred by individual plant resistance genes, an enhanced understanding of the plant immune system is necessary for the longterm development of effective disease management strategies. Current research is rapidly advancing our understanding of the plant innate immune system, with this multidisciplinary subject area reflected in the content of the 18 papers in this Special Issue.
Scope Advances in specific areas of plant innate immunity are highlighted in this issue, with focus on molecular interactions occurring between plant hosts and viruses, bacteria, phytoplasmas, oomycetes, fungi, nematodes and insect pests. We provide a focus on research across multiple areas related to pathogen sensing and plant immune response. Topics covered are categorized as follows: binding proteins in plant immunity; cytokinin phytohormones in plant growth and immunity; plant–virus interactions; plant–phytoplasma interactions; plant–fungus interactions; plant–nematode interactions; plant immunity in Citrus; plant peptides and volatiles; and assimilate dynamics in source/sink metabolism.
Conclusions Although knowledge of the plant immune system remains incomplete, the considerable ongoing scientific progress into pathogen sensing and plant immune response mechanisms suggests far reaching implications for the development of durable disease resistance against pathogens and pests.
Key words: PAMP-triggered immunity, effector-triggered immunity, NLRs, lectins, cytokinins, plant antiviral immunity, phytoplasma, fungi, nematodes, citrus, induced resistance, defensins, terpenoids, source/sink dynamics.
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Section: INNATEIMMUNITY SYSTEMS IN PLANTS
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Structure–function analyses of the domains of plant resistance gene NLRs have so far been limited (Bonardi et al.,2012; Takken and Goverse, 2012). Given that plant NLRs show considerable structural and functional similarities to animal NLRs that are involved in inflammatory and innate immune responses, knowledge of mechanisms involved in activation and regulation of animal NLRs may advance understanding of the action of plant NLRs. In their review, Bentham et al. (2017)
...
 
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Vincent M. Janik  & Laela S. Sayigh
Journal of Comparative Physiology A
DOI 10.1007/s00359-013-0817-7
Abstract:
Bottlenose dolphins (Tursiops truncatus) produce individually distinctive signature whistles that broadcast the identity of the caller. Unlike voice cues that affect all calls of an animal, signature whistles are distinct whistle types carrying identity information in their frequency modulation pattern. Signature whistle development is influenced by vocal production learning. Animals use a whistle from their environment as a model, but modify it, and thus invent a novel signal. Dolphins also copy signature whistles of others, effectively addressing the whistle owner. This copying occurs at low rates and the resulting copies are recognizable as such by parameter variations in the copy. Captive dolphins can learn to associate novel whistles with objects and use these whistles to report on the presence or absence of the object. If applied to signature whistles, this ability would make the signature whistle a rare example of a learned referential signal in animals. Here, we review the history of signature whistle research, covering definitions, acoustic features, information content, contextual use, developmental aspects, and species comparisons with mammals and birds. We show how these signals stand out amongst recognition calls in animals and how they contribute to our understanding of complexity in animal communication.
Keywords Tursiops truncatus - Animal communication - Individual recognition -  Playback - Vocal learning
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Conclusions
The bottlenose dolphin signature whistle clearly is a specific adaptation to ensure individual recognition and social cohesion in a fission–fusion society, where individual rather than group recognition has the highest priority. It is likely that vocal learning evolved in this taxon due to the needs of maintaining and negotiating contact in a noisy environment where sound is the only viable communication channel (Janik and Slater 1997). It remains an unresolved question whether advanced cognition in dolphins evolved in the context of using sounds in a sophisticated way to explore and manipulate their biological and social environments or whether selective pressures for more general skills were responsible. Leaving this question aside, bottlenose dolphins are an interesting study species since they combine many cognitive abilities of the great apes with the communicative versatility that comes with vocal learning (Janik 2013). Further studies are needed to explore how these factors interact and how dolphin communication skills compare to those of the only primate capable of vocal learning, ourselves. When the Caldwells started their signature whistle research 50 years ago, it may have seemed like a less complex signal than what was expected from dolphins at the time. As we have seen though, the signature whistle turned out to be a fascinating case in which each animal introduces a novel call into an existing communication system that is then copied by others to address the whistle owner. Further research is needed to assess how unique this pattern is amongst animals in general, and to investigate underlying cognitive mechanisms for this behavior.
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Admiration and respect go to all living creatures, not only to dolphins. All animals have greater capabilities than we think. Consciousness is more abundant in living creatures. Once, when we will accept this truth as the whole humanity, it will change our behavior as human species for good. Animals and plants are our own brothers and sisters, sharing the same living space. Let us think about them every day.
 
Jiří Kroc
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Richard Wong, Stefan Geyer, Wolfgang Weninger, Jean-Claude Guimberteau & Jason K. Wong
Experimental Dermatology (2015) 25(2)
DOI: 10.1111/exd.12832
Abstract:
The skin is often viewed as a static barrier that protects the body from the outside world. Emphasis on studying the skin's architecture and biomechanics in the context of restoring skin movement and function is often ignored. It is fundamentally important that if skin is to be modeled or developed that we do not only focus on the biology of skin but also aim to understand its mechanical properties and structure in living dynamic tissue. In this review, we describe the architecture of skin and patterning seen in skin as viewed from a surgical perspective and highlight aspects of the microanatomy that have never fully been realized and provide evidence or concepts that support the importance of studying living skin's dynamic behaviour. We highlight how the structure of the skin has evolved to allow the body dynamic form and function; and how injury, disease or ageing results in a dramatic changes to the microarchitecture and change physical characteristics of skin. Therefore, appreciating the dynamic microanatomy of skin from the deep fascia through to the skin surface is vitally important from a dermatological and surgical perspective. This focus provides an alternative perspective and approach to addressing skin pathologies and skin ageing.This article is protected by copyright. All rights reserved.
Key words: ageing – architecture – dynamic anatomy – patterning – skin
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Paper -- future applications of this research.
During my PhD research on modeling of Dynamic Recrystallization, I came across the Sakai & Jonas review paper on DRX. It helped me to develop a successful model of it, that is the first which had explained the mechanism of several centuries observed phenomena. Without this evidence provided in the review, nothing can be accomplished.
A very similar situation is with your review, dear Authors of the above-mentioned paper.
A researcher who wants to build a realistic model of fascia based model of skin will find your paper as a kicker that helps to reach a higher orbit in solving the problem.
As a mathematician working in complex systems, using mathematical modeling to describe natural phenomena, I have to mention several insights reached during reading your paper:
1. The phenomenon fails in the class of Complex Systems phenomena.
2. Agent-based modeling combined with networks seems to be a good starting point to build a prototypical model.
3. Cellular Automata seems to be to have too much fine granularity for this task.
4. Actual positions of end-points should be stored only. It will save a lot of memory and computational power!
5. A good idea would be to study non-newtonian liquids, as they help to gain a better insight into the physics related to functions of the fascia.
6. This is a great place to work, as it can help to develop a methodology that will be used in modeling of other parts of human bodies, including all organs.
7. While seeing this review, I wished to be at the PhD research again. A challenging, yet very rewarding task.
8. Back to point 5, viscoelasticity is a very exciting area of research that will bring surprising insights into the real functioning of cells and bodies.
 
Jiří Kroc
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Hiroki Sayama
State University of New York at Binghamton
(2015) Open SUNY, ISBN 13: 9781942341093
Keep up to date on Introduction to Modeling and Analysis of Complex Systems at http://bingweb.binghamton.edu/~sayama/textbook/
About the Book
Introduction to the Modeling and Analysis of Complex Systems introduces students to mathematical/computational modeling and analysis developed in the emerging interdisciplinary field of Complex Systems Science. Complex systems are systems made of a large number of microscopic components interacting with each other in nontrivial ways. Many real-world systems can be understood as complex systems, where critically important information resides in the relationships between the parts and not necessarily within the parts themselves.
This textbook offers an accessible yet technically-oriented introduction to the modeling and analysis of complex systems. The topics covered include: fundamentals of modeling, basics of dynamical systems, discrete-time models, continuous-time models, bifurcations, chaos, cellular automata, continuous field models, static networks, dynamic networks, and agent-based models. Most of these topics are discussed in two chapters, one focusing on computational modeling and the other on mathematical analysis. This unique approach provides a comprehensive view of related concepts and techniques, and allows readers and instructors to flexibly choose relevant materials based on their objectives and needs. Python sample codes are provided for each modeling example.
Table of Contents
• Introduction
• Fundamentals of Modeling
• Basics of Dynamical Systems
• Discrete-Time Models I: Modeling
• Discrete-Time Models II: Analysis
• Continuous-Time Models I: Modeling
• Continuous-Time Models II: Analysis
• Bifurcations
• Chaos
• Interactive Simulation of Complex Systems
• Cellular Automata I: Modeling
• Cellular Automata II: Analysis
• Continuous Field Models I: Modeling
• Continuous Field Models II: Analysis
• Basics of Networks
• Dynamical Networks I: Modeling
• Dynamical Networks II: Analysis of Network Topologies
• Dynamical Networks III: Analysis of Network Dynamics
• Agent-Based Models
Read more about Complex System in the project:
 
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Jiri Kroc
preprint, February 8, 2022
The link to the paper:
Abstract:
The current frontiers in the description and simulation of advanced physical and biological phenomena observed within all scientific disciplines are pointing directly toward the importance of having robust models that are error resilient. Complexity research is lacking deeper knowledge of the design methodology of such processes that are capable to recreate the observed robustness. The first part provides a concise introduction into this difficult research area to non-specialists. This is followed by the second part of the paper, which is focusing on a description, that is providing a certain level of the desired robustness. The first introductory part is describing the basic principles that are demonstrated on a simple cellular automaton having an extremely simple updating rule, which was created by John Conway: the 'Game of Life' (aka the GoL). This allows us to enter the second, research part dealing with a simple CA rule, which is a generalization of the GoL, that is possessing an increased robustness against errors along with a very interesting set of emergent structures that are capable of unexpectedly long-range synchronization.
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The link to the open-source 'Game of Life' cellular automaton software in Python:
***
The link to the open-source generalized, robust ''Game of life' software in Python:
***
Tlink to sample runs of generalized, robust ''Game of life' (above):
 
Jiří Kroc
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Jiri Kroc
Motivation
Everyone who is carrying on research in the intersection of biology, mathematics, and computations is very well aware of our inability to capture the processing of information within biological structures properly.
Therefore, the simulation of GoL presented in this share, along with other shares of other authors, aims to raise the attention of the general scientific community about the above-mentioned intersection.
Surprisingly, when the right mathematical formalism is found, apparently very complicated emergent processes can be described by quite simple mathematical descriptions, as is exactly happening in the 'Game of Life' and similar computational models that are all expressing unprecedented complexity.
Description
This is a preliminary research output, which occurred as a side result during research on modifications of the 'Game of Life' proposed by John Conway. Such scientifically and visually appealing simulation had arisen among many others where the observed structures might be interesting to other researchers. More will appear in a couple of months, stay tuned.
In general, it is observed that emergent structures of various types arise within this specific cellular automaton, all of them are having period of two. What is surprising is the fact that those structures are long range correlated, and some of them even turn by ninety degrees. From a certain point of view, we can say that the observed emergents posses a very stable binary behavior that deserves a deeper interest. Surprisingly, no moving emergents were observed yet in this type of cellular automaton.
More videos and the code will occur here:
A sample video from an ongoing research:
 
Jiří Kroc
added a research item
The presented emergent structures were discovered during research on modifications of the 'Game of Life' proposed by John Conway, which are aiming towards discovery of robust emergents, that are immune to randomly injected faulty evaluations. See details in the paper, the link is provided below, where those simulations are presented only in figures. Many scientifically and visually appealing simulation had arisen there, where the observed structures might be interesting to researchers working in biology and other disciplines. Animations are always having a great expressive power, see PNG animations below. Make sure that the viewer can display animated PNG figures! In general, it is observed that emergent structures of various types arise within this specific cellular automaton, all of them are having the period of two. What is surprising is the fact that those structures are long-range correlated, and some of them even turn by ninety degrees. From a certain point of view, we can say that the observed emergents posses a very stable binary behavior that deserves a deeper study. Surprisingly, no moving emergents were observed in this type of cellular automaton. ............ The publication along with the Python software and animations are available at the link: https://www.researchgate.net/publication/361818826_Robust_massive_parallel_information_processing_environments_in_biology_and_medicine_case_study
Jiří Kroc
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YOGESH CHANDRA TRIPATHI, Rakesh Kumar, Vinay Varshney & Sanjay Naithani
ENVIS Forestry Bulletin 10  (Jan 2010) 114-121
Abstract
The universe has increasingly become chemicalized primarily due to the introduction of various chemicals in almost all processes of life and ecosyem. Agriculture and health are the major sector where chemicals in the form of pesticides, fertilizers and disinfectants are extensively used. The human population is exposed to these chemicals primarily through the consumption of pesticide contaminated farm produce leading to long term health hazards. The ill effects of chemicals in humans can be managed by intake of vital phytochemicals including phytonutrients, antioxidants and other therapeutic plant products.
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Prevention encompass vitamins, dietary antioxidants, and phenolics from spices, which are listed in the paper.
This information is vital for achieving better health in the situation that we do have to consume food that is containing pesticides and other harmful substances. Our health us the greatest treasure of our lives.
Have a great health and productive life :-)
 
Jiří Kroc
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The following research ideas had been achieved while reading the following paper that describes the principles of synthesis of biomolecules from prebiotic substances.
The Transformation by Catalysis of Prebiotic Chemical Systems to Useful Biochemicals: A Perspective Based on IR Spectroscopy of the Primary Chemicals: Solid-Phase and Water-Soluble Catalysts
Ragnar Larsson & Abdul Malek
Applied Sciences 11(2021) 10125, DOI: 10.3390/app112110125
While reading this extraordinary paper, suddenly quite a few things fit together. Suddenly, a lot of observed effects in biology make the sense. Those who want to pursue research on functioning of real biological systems might be interested about the following ideas:
* This research might become the beginning of the next stage of biomedical research and praxis, as it incorporates minuscule reactions that are staying at the core and behind all of all biological processes.
* Researchers working in the area of computational biology, complex systems, catalytic reactions, cellular automata, agent based modeling, synthesis of biomolecules should join their efforts on building models of artificial biomolecular models that will help to understand certain metabolic diseases and beyond.
* Such models can become a computational testing ground of various hypotheses on functioning biological systems in health and disease.
* Various chemical and environmental disruptors can be tested in silico using the above-mentioned models.
* Those who are working on catalytic reactions can employ change of light frequency on production of biomolecules. Is there a chance to find a reaction that will produce as the 'waste' hydrogen atoms or molecules? When successful, could this revolutionize industrial energy production?
* It can be other molecules like methane that are packing a lot of energy when burned.
* The possibility to change the synthesis of biomolecules by mere change of light wavelength has a great impact on our understanding of artificial light on human health.
* Are we becoming ill due to lack of certain light frequencies, which are fundamental to synthesize certain biomolecules and proteins?
* Can we build artificial organs, employing the principles described in the paper?
* Can we improve industrial production of biomolecules that are having the right quantum composition and hence, are natural to human bodies?
There are more similar ideas. Do not hesitate to contact me or make comments. We are here to help each other. Together, we can achieve a lot.
Have a Merry Christmas and happy New Year :-)
 
Jiří Kroc
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Ragnar Larsson & Abdul Malek
Applied Sciences 11(2021) 10125, DOI: 10.3390/app112110125
Abstract:
This study is a continuation of our research on understanding the possible chemical routes to the evolution of life on earth based on the “Selective Energy Transfer” (SET) theory. This theory identifies the specific vibrational mode of the catalyst that is in energy-resonance with a suitable vibrational mode of the reactant. In this way, energy is transferred from catalyst to reactant up to the energy of activation, making possible a particular chemical outcome. Then, we extend this model to the mostly unknown and highly complex environment of the hydrothermal vents, to speculate how prebiotic chemicals, necessary for the evolution of life, could have formed. It is to the credit of the SET theory that it can reflect the slight difference in the catalytic system that gives dramatically very different chemical outcome. It is shown, here, how in model laboratory experiments, methanol gives dimethyl ether (DME) in a 100% yield with Cu exchanged montmorillonite as the catalyst, or a very different product methyl formate (MF) in lower yields, with another Cu2+ ion-exchanged clay mineral (laponite) as the catalyst system. We also show, based on standard laboratory experiments, how COS (carbonyl sulfide) with a strong absorption band at 2079 cm−1 by itself and/or catalyzed by montmorillonite with strong Si-O-Si asymmetric vibration of 1040 cm−1 can react with alpha-amino acids to form alpha-amino acid thiocarbamate (AATC), which we feel could represent the most primitive analogue to coenzyme A (CoASH), a highly versatile bio-enzyme that is vital both for the metabolism and the synthesis of biochemicals in the living system. AATC itself may have undergone evolutionary developments through billions of years to transform itself into coenzyme A (CoASH) and its acetyl ester analogue acetyl coenzyme A (ACoA).
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From the Conclusions:
... Furthermore, in this study, we have investigated the possibility of finding the building stones of molecules that we now know are necessary for life. We have found catalysts that can transform simple compounds of only a few atoms to larger units of a complex structure. Thus, for example, COS can catalyze the formation of all the molecules that together form the bioactive chains of RNA. COS can also combine with other molecules such as amino acids to act in a liquid state to build bioactive substances, and last but not the least, montmorillonite can act as a solid catalyst in aqueous media, to form molecules that seem to be of a life creating kind.
Since COS originates from volcanic eruptions and montmorillonite is formed from petrified lava, eroded by rainwater [11], we can state that many catalysts, shaped in nature, are related to the volcanic activity of the young planet. Now, these catalysts seem to be necessary for life, and we suggest that life as we know it has had a volcanic background. This is in perfect agreement with the considerations of Orgel et al. [30] and of M. Schirber [39,40].
 
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Try the approach described in the below provided paper in order to observe changes of the complexity of the by-the-third-party given data. You will compare new data with data having a known source, and you will know immediately whether the input data are genuine or not!
A deep forensic analysis of the input data is crucial in making sure that the following research is valid.
Methods to use complexity measures based on entropy and an application are described in this paper:
 
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Robert T. Wainwright
Many of us are wondering: "Why is there existing a link between the theory of complex systems and living entities?" The 'Game of Life' encoded in a primitive computing environment and the paper presented here give the answer to everyone who wants to know more.
This paper represents the simplest possible proof of capabilities of complex systems to carry out universal computing with the equivalence to the Turing machine. This paper gives a proof that we are capable to build computers or computing environments within any complex system that has sufficient flexibility. Life entities posses such and even greater levels of complexity.
Those interested about the open source code of the 'Game of Life' can download it here:
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Read more about the paper here (including the PDF link):
 
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Alina  Yuryevna  Maslova, Kheda  Lechaevna  Bazaeva,   Zaira  Arazovna  Abdullaeva,  Shuainat  Omarovna Khazamova,   Karina  Akhmedovna  Zeusheva,  Tatiana  Alekseevna  Grechkina,   Evgeniya  Nikolaevna  Semkina, Maksim  Alekseevich  Abramov,   Artem  Evgenevich  Mishvelov  and Sergey Nikolaevich Povetkin
Journal of Pharmaceutical Research International 33(33A):60-68 (June 2021)
DOI: 10.9734/JPRI/2021/v33i33A31772
Abstract
At present, research in the field of the brain does not cease to surprise us with new facts and discoveries that no one could have suspected about 30 years ago. But it was at the time when it became clear that the cerebral neurons are not the only cells that can respond to changes in the external environment. A real scientific boom began to study a heterogeneous group called glia. And scientists are paying close attention to the largest of them – astrocytes. Understanding the importance of astrocytes in the mechanisms of repair and damage to brain cells in various forms of CNS pathology determines the possibility of targeted search for drugs that affect the rate of development of reactive astrogliosis in response to various brain injuries. At the same time, pharmacological modulation of activated astrocytes and other components of glia can be an integral part of the therapy of neurological diseases.
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CONCLUSION 
Astrocytes and other cellular elements of glia in the central nervous system have multidirectional functions that contribute to both the survival of neurons and their delayed damage. Astroglial reactivity is manifested by the ability of astrocytes to repair various CNS lesions. However, a glial scar consisting of activated astrocytes can determine various neurotoxic effects that inhibit the repair of neurons and the regeneration of axons. In ischemia, traumatic brain injury, or neurodegenerative diseases, astrogliosis may be modulated. Understanding the importance of astrocytes in the mechanisms of repair and damage to brain cells in various forms of CNS pathology determines the possibility of targeted search for drugs that affect the rate of development of reactive astrogliosis in response to various brain injuries. At the same time, pharmacological modulation of activated astrocytes and other components of glia can be an integral part of the therapy of neurological diseases.
 
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Meng Zhou & Jiang Zhao
A selection from the paper:
Perspectives:
"In recent years, the gut microbiota of host has received more attention. Generally, the dysbiosis of gut microbiota often occurs simultaneously with the metabolic disorder of host. The studies on the health effects of host based on the changes in gut microbiota and metabolic profile have been continuously reported. In the past few decades, the pesticides have been widely used, and their toxic effects on the non-target organisms have received increasing attention. In particular, some studies have confirmed the destructive role of pesticides on the gut microbiota and metabolic profile of host. Unfortunately, most of these studies have only established a simple correlation between the pesticides and host gut microbiota and metabolic profile, while the key roles of the gut microbiota and metabolic profile host in the pesticide-induced toxic effects are still not focused. In particular, some studies have shown that some specific bacteria in gut microbiota can regulate specific metabolites or specific metabolic pathways, further affecting the host health. However, the current studies on the toxic effects of pesticides have not established a clear relationship between the specific pesticides and specific gut microbiota or metabolites. On the other hand, the key role of the gut microbiota and metabolic profile of host in the pesticide-induced toxic effect is needed to be further confirmed either by the transplantation of microbiota or the dietary supplementation of specific metabolites. In summary, this study reviewed the studies on the toxic effects of pesticides based on the gut microbiome and metabolomics of host. This review further emphasized on the role of changes in the gut microbiome and metabolomics of host in the pesticide-induced host toxic effects."
When interested everyone is welcomed to read more:
 
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Svein Linge & Hans Petter Langtangen
Scientific computing has gained an increasing importance in all scientific fields over the past several decades. Python become of one the workhorses of this development. Python is easier to learn when compared to C/C++ and has a huge amount of modules extending its capabilities.
This open access book provides a very useful recipe to design your own software by demonstrating Python programs on real scientific applications. This book is highly recommended to everyone who means it with Python programming seriously and want to write down reliable and precise Python software. More books like this one will follow in the future in this project (stay tuned and follow the project when interested).
Good luck at your own programming!
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Those interested can find more at the link:
 
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Aparna Rai, Pramod Shinde, and Sarika Jalan
Applied Network Science 3(1) (December 2018)
DOI: 10.1007/s41109-018-0107-y
Abstract
The fundamental understanding of altered complex molecular interactions in a diseased condition is the key to its cure. The overall functioning of these molecules is kind of jugglers play in the cell orchestra and to anticipate these relationships among the molecules is one of the greatest challenges in modern biology and medicine. Network science turned out to be providing a successful and simple platform to understand complex interactions among healthy and diseased tissues. Furthermore, much information about the structure and dynamics of a network is concealed in the eigenvalues of its adjacency matrix. In this review, we illustrate rapid advancements in the field of network science in combination with spectral graph theory that enables us to uncover the complexities of various diseases. Interpretations laid by network science approach have solicited insights into molecular relationships and have reported novel drug targets and biomarkers in various complex diseases.
***
Complex networks that are operating in biological cells, tissues, organs, and bodies are fundamental for understanding, manipulation, and treatment of diseases. This paper explains basic principles that are applied in studying those networks and how that can help to understand the root causes of diseases. Because complex networks are very hard to understand in their functions, due to their inherently emergent properties, we need tools like spectral analysis to localize the fundamental processes undergoing within them.
From the conclusion:
"Overall, spectral graph theory framework has helped in uncovering the complexity at the fundamental level enabling us to have a global view of the diseasome. However, the understanding of the biological phenomenon in disease networks using graph spectra is still at the budding stage. The studies using graph spectra can help in improving our current knowledge of molecular associations in disease models in a timeefficient and cost-effective manner. Employing such a technique has already shown its promise lead to further advancements in disease diagnosis, prognosis, and identification of novel drug targets for disease therapy. This novel approach provides a clue to developing the promising and nascent concept of single drug therapy for multiple diseases, biomarkers useful in disease diagnosis as well as personalized medicine. The holistic framework of networks together with the spectral analysis may be useful for diseases wherein the knowledge of the abnormal gene/protein(s) function(s) is unavailable."
 
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Nick J. Spencer, Lee Travis, Lukasz Wiklendt, Marcello Costa, Timothy J. Hibberd, Simon J. Brookes, Phil Dinning, Hongzhen Hu, David A. Wattchow, and Julian Sorensen
From the discussion:
"The data suggest that immediately prior to, and during the aboral propulsion of content, there is temporally coordinated activation of excitatory and inhibitory motor neurons, by a chain of shared interneurons. Importantly, despite coordinated activation of the ENS along the length of colon, colonic smooth muscle
does not contract simultaneously during aborally propagating CMCs. The findings show this is because descending inhibitory pathways are strongly activated from the contractile region, leading to inhibition of the smooth muscle aborally. This is supported by the experiments using L-NOARG, which caused a
large increase in EJP synchronization and action potential firing, in the region aboral to the contraction. Therefore, descending inhibitory pathways act to suppress downstream the excitation that is activated in parallel. This may correspond to the descending inhibition that was described by Bayliss and Starling in
1900, which may serve as a receptive relaxation, facilitating aboral propulsion of content. The effects of atropine, which abolished EJPs and revealed simultaneous IJPs, is also consistent with this mechanism. How the CMC contraction propagates into this area of inhibition is not clear."
"These results uncover primordial circuity in the ENS, which when activated by a variety of stimuli and a variety of experimental recording conditions (and independent of the mechanical states of the musculature) triggers a hard-wired neural pathway that discharges at ~2 Hz for ~20–30 seconds. Distension across the full length of colon was not a prerequisite for synchronization of the ENS circuits underlying propulsion. Furthermore, once elicited, the coordinated and repetitive activation of the ENS still maintains at firing rate of ~2 Hz, even though the colon can be partially contracted and lacks all movement of content. We have now revealed that a robust ENS circuit underlies both propulsive and non-propulsive behaviours (Fig. 10)."
 
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Arieh Ben-Naim
Only by going to the roots of the entropy definition, scientists can recognize its importance, scope of its validity, and when it is misused. This paper is very helpful in elucidating the above-mentioned issues using clear, easy to follow reasoning that is accessible even to non-specialists.  
Those who are interested can read more at the link:
 
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Johannes Lehmann, Jose Pereira da Silva Jr., Christoph Steiner, Thomas Nehls, Wolfgang Zech, and Bruno Glaser
Local, sustainable agriculture can benefit from the information covered in this paper dealing with ancient soils called Anthrosol.
From the text:
"The high fertility of the prehistoric Anthrosols may have been more related to nutrient release from successively available soil pools than high ion contents at exchange sites. Without fertilization, the leachate in the Anthrosols had extremely low concentrations of nutrients while nutrient availability was high compared to the Ferralsol. Low leaching at high nutrient availability ensures sustainable soil fertility. These results coincide with observations made by Petersen et al.(2001) who found Anthrosols in Western Amazônia which have been under continuous cultivation without fertilization for 40 years."
"The demonstrated properties of the relict anthropogenic soils have important implications for soil management of Ferralsols indicating that organic applications ca be used for sustainable crop production under humid tropical conditions. On the other hand, these results also imply that such Anthrosols should not be fertilized with inorganic nutrients but organic applications be continued."
Read more at the following link:
 
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Ling-Wei Kong, Hua-Wei Fan, Celso Grebogi, and Ying-Cheng Lai
Physical Review Research 3(1) 013090 (2021)
DOI: 10.1103/PhysRevResearch.3.013090
Abstract
To predict a critical transition due to parameter drift without relying on a model is an outstanding problem in nonlinear dynamics and applied fields. A closely related problem is to predict whether the system is already in or if the system will be in a transient state preceding its collapse. We develop a model-free, machine-learning-based solution to both problems by exploiting reservoir computing to incorporate a parameter input channel. We demonstrate that, when the machine is trained in the normal functioning regime with a chaotic attractor (i.e., before the critical transition), the transition point can be predicted accurately. Remarkably, for a parameter drift through the critical point, the machine with the input parameter channel is able to predict not only that the system will be in a transient state, but also the distribution of the transient lifetimes and their average before the final collapse, revealing an important physical property of transient chaos.
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Prediction of systems transition and their collapse from signals that they are generating, without knowledge of the system themselves is a very difficult problem. Biology and medicine will greatly benefit from being able to predict systems collapses.
This is exactly why this research got shared in this project. It should disseminate knowledge about advanced methods capable to predict the future evolution of the systems.
 
Jiří Kroc
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Eneko Osaba and Xin-She Yang
in the book: Applied Optimization and Swarm Intelligence
Editors: Eneko Osaba and Xin-She Yang
Springer (January 2021)
Part of the Springer Tracts in Nature-Inspired Computing
DOI: 10.1007/978-981-16-0662-5
Abstract
This book gravitates on the prominent theories and recent developments of swarm intelligence methods, and their application in both synthetic and real-world optimization problems. The special interest will be placed in those algorithmic variants where biological processes observed in nature have underpinned the core operators underlying their search mechanisms. In other words, the book centers its attention on swarm intelligence and nature-inspired methods for efficient optimization and problem solving. The content of this book unleashes a great opportunity for researchers, lecturers and practitioners interested in swarm intelligence, optimization problems and artificial intelligence.
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A very important introduction into swarm optimization techniques with up-to-date references to the most important applications, software, and hints for the future research.
Every decision maker in the research should be aware of those techniques as it can speed up research in virtually any area including biology & medicine.
Young researchers can benefit from this knowledge tremendously as they do not loose valuable time, effort, and funds on trial and error experiments and theories. Optimization helps to localize the best parameters that are most affecting the observed phenomena.
 
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John B Calhoun
Proc. Roy. Soc. Med. Volume 66 (January 1973) 80-88.
Conclusion
The results obtained in this study should be
obtained when customary causes of mortality
become markedly reduced in any species of
mammal whose members form social groups.
Reduction of bodily death (i.e. 'the second death')
culminates in survival of an excessive number of
individuals that have developed the potentiality
for occupying the social roles characteristic of the
species. Within a few generations all such roles in
all physical space available to the species are
filled. At this time, the continuing high survival
of many individuals to sexual and behavioural
maturity culminates in the presence of many
young adults capable of involvement in appro-
priate species-specific activities. However, there
are few opportunities for fulfilling these poten-
tialities. In seeking such fulfilment they compete
for social role occupancy with the older established
members of the community. This competition is
so severe that it simultaneously leads to the nearly
total breakdown of all normal behaviour by both
the contestors and the established adults of both
sexes. Normal social organization (i.e. 'the estab-
lishment') breaks down, it 'dies'.
Young born during such social dissolution are
rejected by their mothers and other adult asso-
ciates. This early failure of social bonding
becomes compounded by interruption of action
cycles due to the mechanical interference resulting
from the high contact rate among individuals
living in a high density population. High contact
rate further fragments behaviour as a result of the
stochastics of social interactions which demand
that, in order to maximize gratification from social
interaction, intensity and duration of social
interaction must be reduced in proportion to the
degree that the group size exceeds the optimum.
Autistic-like creatures, capable only of the most
simple behaviours compatible with physiological
survival, emerge out of this process. Their spirit
has died ('the first death'). They are no longer
capable of executing the more complex behaviours
compatible with species survival. The species in
such settings die.
For an animal so simple as a mouse, the most
complex behaviours involve the interrelated set of
courtship, maternal care, territorial defence and
hierarchical intragroup and intergroup social
organization. When behaviours related to these
functions fail to mature, there is no development
of social organization and no reproduction. As
in the case of my study reported above, all members of the population will age and eventually die.
The species will die out.
For an animal so complex as man, there is no
logical reason why a comparable sequence of
events should not also lead to species extinction.
If opportunities for role fulfilment fall far short
of the demand by those capable of filling roles,
and having expectancies to do so, only violence
and disruption of social organization can follow.
Individuals born under these circumstances wilt
be so out of touch with reality as to be incapable
even of alienation. Their most-complex behaviours
will become fragmented. Acquisition, creation
and utilization of ideas appropriate for life in a
post-industrial cultural-conceptual-technological
society will have been blocked. Just as biological
generativity in the mouse involves this species'
most complex behaviours, so does ideational
generativity for man. Loss of these respective
complex behaviours means death of the species.
Mortality, bodily death = the second death
Drastic reduction of mortality
=death of the second death
=death squared
=(death)2
(Death)2 leads to dissolution of social organization
=death of the establishment
Death of the establishment leads to spiritual death
=loss of capacity to engage in behaviours essential to
species survival
=the first death
Therefore:
(Death)2 =the first death.
Happy is the man who finds wisdom,
and the man who gains understanding.
Wisdom is a tree of life to those who
lay hold of her.
All her paths lead to peace.
(Proverbs iii.13, 18 and 17, rearranged)
***
This older, yet still very up-to-date research made a deep probe into inner workings of societies that are rising, culmination, stagnating, and ultimately declining. I do not recommend reading it to sensitive people.
 
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Vineet Kumar, RK Naresh, Sumit Kumar, Sunil Kumar, Arvind Kumar, RK Gupta, RS Rathore, SP Singh, Ashish Dwivedi, Saurabh Tyagi, and NC Mahajan
Journal of Pharmacognosy and Phytochemistry 2018; 7(1): 585-597
Abstract
The challenge that the world is facing has been to maximize food production to feed the increasing population. Further, agriculture at present encompasses many problems such as stagnating food-grain production, multi-nutrient deficiency, declining fertilizer response, reduction in land availability for cultivation, environmental pollution and land degradation. To manage long term soil fertility, productivity as well as environment quality, efficient nutrient management practices integration can be the most sustainable practices to adopt. Among plant nutrients, nitrogen (N) is the most important. Its importance as a growth-and yield-determining nutrient has led to large and rapid increases in N application rates, but often with poor use efficiency. Nitrogen management requires special attention in its use so that the large losses can be minimized and the efficiency maximized. Site-specific nutrient management (SSNM) has been found especially useful to achieve the goals of improved productivity and higher N use efficiency (NUE). Leaf color charts and chlorophyll meters assist in the prediction of crop N needs for rice and wheat, leading to greater N-fertilizer efficiency at various yield levels. Remote sensing tools are also used to predict crop N demands precisely. At the same time, traditional techniques like balanced fertilization, integrated N management (INM), split application and nutrient budgeting, among others, are also used to supplement recent N management techniques to attain higher productivity and NUE, and reduce environmental pollution through the leakage of fertilizer N.This will definitely enhance the productivity of rice and wheat crops by improving soil fertility and ameliorating adverse soil physical conditions. This paper reviews the effect of efficient nutrient management practices on sustaining soil health improving the productivity of Rice-wheat cropping sequence.
***
Soil health and human health are highly interconnected in many ways: through their respective microbiota. Microbiota of human gut is highly affected by agricultural chemicals. By keeping our fields healthy, we keep healthy people. This paper explains techniques of nitrogen supplementing to the filed that keep soul healthy and crops high.
 
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Chris Fields and Michael Levin
This paper is very interesting to all who want to understand the rise of diseases with respect to morphological changes, target morphology, and complex systems links. A good starting point to all who are interested about this frontier research area. All medical practicioners can benefit from the knowledge covered here as it links holistic approaches with modern medical science.
 
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Federico E. Turkheimer, Peter Hellyer Angie A. Kehagia, Paul Expert, Louis-David Lord, Jakub Vohryzek,
Jessica De Faria Dafflon, Mick Brammer, and Robert Leech
April 2019Neuroscience & Biobehavioral Reviews 99
DOI: 10.1016/j.neubiorev.2019.01.023
Abstract
The concept of "emergence" has become commonplace in the modelling of complex systems, both natural and man-made; a functional property" emerges" from a system when it cannot be readily explained by the properties of the system's sub-units. A bewildering array of adaptive and sophisticated behaviours can be observed from large ensembles of elementary agents such as ant colonies, bird flocks or by the interactions of elementary material units such as molecules or weather elements. Ultimately, emergence has been adopted as the ontological support of a number of attempts to model brain function. This manuscript aims to clarify the ontology of emergence and delve into its many facets, particularly into its "strong" and "weak" versions that underpin two different approaches to the modelling of behaviour. The first group of models is here represented by the "free energy" principle of brain function and the "integrated information theory" of consciousness. The second group is instead represented by computational models such as oscillatory networks that use mathematical scalable representations to generate emergent behaviours and are then able to bridge neurobiology with higher mental functions. Drawing on the epistemological literature, we observe that due to their loose mechanistic links with the underlying biology, models based on strong forms of emergence are at risk of metaphysical implausibility. This, in practical terms, translates into the over determination that occurs when the proposed model becomes only one of a large set of possible explanations for the observable phenomena. On the other hand, computational models that start from biologically plausible elementary units, hence are weakly emergent, are not limited by ontological faults and, if scalable and able to realistically simulate the hierarchies of brain output, represent a powerful vehicle for future neuroscientific research programmes.
***
The origins of higher cognitive functions and consciousness are still enigmatic to science. Science is progressing towards better understanding of those phenomena.
All who would like to know more about the program of weak emergence models describing brain functions should be aware of this publication giving a brief and clear introduction into this exciting subject.
 
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David J. Chalmers
In P. Davies & P. Clayton (eds.), The Re-Emergence of Emergence: The Emergentist Hypothesis From Science to Religion. Oxford University Press (2006)
(PDF)
Abstract
The term ‘emergence’ often causes confusion in science and philosophy, as it is used to express at least two quite different concepts. We can label these concepts _strong_ _emergence_ and _weak emergence_. Both of these concepts are important, but it is vital to keep them separate
***
This paper helps to dive into the concept of emergence to all those who are interested about it and doesn't have mathematical education quite easily. It is presented in the accessible language. Highly recommended to all as an introduction into the topic.
 
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S J Malik, B.B. Gunjal, Srinivas Kasulla, and Aparna Gunjal
DSTA 65th Annual Convention, At: Pune, Maharashtra, India (October 2019)
Abstract
It takes millions of years for dead organisms to get converted into fuels. Continuous usage of
these fuels is the major concern as these fuels are fast depleting. BioCNG is the purified form of biogas where all the unwanted gases are removed to produce (>96%) pure methane gas. BioCNG is exactly similar to the commercially available natural gas. This paper reviews the production of BioCNG from Press Mud. Based on the studies in respect of techno commercial analysis for BioCNG production from 100 TPD Press Mud plant, the project is technically feasible and commercially viable.
***
This profitable project can bring the attention to all decision makers who are working in industries that have biological waste that can be converted into methane. It is a win-win situation for business, people, and our ecosystems.
Please share with everyone who might be interested in this project. Thank you.
 
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Michael Levin
The Scientists (September 2020)
Understanding biology’s software—the rules that enable great plasticity in how cell collectives generate reliable anatomies—is key to advancing tissue engineering and regenerative medicine.
About the author:
Michael Levin is the director of the Allen Discovery Center at Tufts University and Associate Faculty at Harvard University’s Wyss Institute. Email him at michael.levin@tufts.edu. M.L. thanks Allen Center Deputy Director Joshua Finkelstein for suggestions on the drafts of this story.
***
This easy to read story about novel research on biocircuits that are playing a very important role in morphological growth, tissue repair, and regrowth of limbs and organs. We are at the brink of an exciting stage of human medicine. It can cause a revolution in reconstructive medicine, transplantology, and healing of long term diseases. This is exactly the type of information, which is nicely packed, that you do not like to miss.
 
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Arturo Vittori
An idea to harvest water from the thin air using harvesting towers, which are having a special shape & fabric enabling condensation, that is employing different temperatures during day and night. No energy resources are used in the condensation. It is done automatically by physical processes.
The web page of the project:
A video explaining collecting water in arid areas. Many people living in dry climates will benefit from this information.
Please share with others. Those towers can save lives of many people having water shortages. Thank you.
 
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Cowpathy and Vedic Krishi to Empower Food and Nutritional Security and Improve Soil Health: A Review RK Naresh, AK Shukla, Mukesh Kumar, Arvind Kumar, RK Gupta, Vivek, SP Singh, Purushattom, PK Singh, Yogesh Kumar, SP Singh, SS Tomar, Vineet Singh, RC Rathi, NC Mahajan, Sunil Kumar and Satyaveer Singh Journal of Pharmacognosy and Phytochemistry 2018; 7(1): 560-575. (January 2018) https://www.researchgate.net/publication/322469720_Cowpathy_and_Vedic_Krishi_to_Empower_Food_and_Nutritional_Security_and_Improve_Soil_Health_A_Review https://www.phytojournal.com/archives/?year=2018&vol=7&issue=1&ArticleId=2549 Abstract and figures The study aims to evaluate the efficiency and efficacy of some cowpathy and vedic krishi inputs, viz. Vrkshayurveda, Panchagavya, Kunapajala, Beejamrit, Jeevamirit, Compost tea, Matka khad, Vermiwash and Amrutpani with the objectives to enhance the biological efficiency of crop plants and food production for eco-friendly nutrient and disease management and improve soil health in organic farming. Cowpathy and vedic krishi techniques are low input costs, which comply well with the ecological and socioeconomic conditions of vast segment of farming community comprising of small and marginal farmers. All the Cowpathy and vedic krishi inputs were found quite effective in enhancing the productivity of different crops and suppressing the growth of various plant pathogens by producing antibacterial and anti-fungal compounds, hormones and siderophores. Application of vermiwash gave 60, 10, 26 and 27% higher yield in Knol khol (211.67qha-1), onion (177.81qha-1), French-bean (16.3qha-1 seed yield), Pea (16.3qha-1) and Paddy (28.45qha-1), respetively over control. Panchagavya 6 per cent spray recorded significantly higher Capsicum fruit yield (30.25, 37.49, 48.91, 118.91, 96.15, 86.29, 47.81 q ha-1 at 60, 70, 80, 90, 100, 110 and 120 DAT, respectively), N-fixers life (23.68, 25.59 at 60 DAT and 17.77, 17.18 X 103 at harvest during kharif and summer, respectively). Application of kunapajala (T-3) treatment was effective in enhancing the morphological parameters of the leaves of tomato plant followed by conventional farming (T-1) and organic farming (T-2).The beneficial microorganisms from Panchagavya and their establishment in the soil improves soil fertility and provide food grains free from the health hazards of using chemical fertilizers/ pesticides.Vermiwash, Beejamrit, and Jeevamirit as foliar were also proved quite effective in enhancing the productivity of different crops and effective against various plant pathogens. *** A very important review on ecologically friendly and human friendly food that can be produced using traditional agricultural procedures developed over millennia of existence of agriculture. A highly recommended contribution to all professionals who are open to new ideas. This review can serve as a recipe to discover approaches suitable to any country, climate, and conditions. Thank you authors for providing us such great insight into this highly important part of our lives. We now know that good is defining the diversity and quality of our gut microbiota, which in turn defined our health. Your approach is gut microbiota friendly.
RK Naresh, AK Shukla, Mukesh Kumar, Arvind Kumar, RK Gupta, Vivek, SP Singh, Purushattom, PK Singh, Yogesh Kumar, SP Singh, SS Tomar, Vineet Singh, RC Rathi, NC Mahajan, Sunil Kumar and Satyaveer Singh
Journal of Pharmacognosy and Phytochemistry 2018; 7(1): 560-575. (January 2018)
Abstract and figures
The study aims to evaluate the efficiency and efficacy of some cowpathy and vedic krishi inputs, viz. Vrkshayurveda, Panchagavya, Kunapajala, Beejamrit, Jeevamirit, Compost tea, Matka khad, Vermiwash and Amrutpani with the objectives to enhance the biological efficiency of crop plants and food production for eco-friendly nutrient and disease management and improve soil health in organic farming. Cowpathy and vedic krishi techniques are low input costs, which comply well with the ecological and socioeconomic conditions of vast segment of farming community comprising of small and marginal farmers. All the Cowpathy and vedic krishi inputs were found quite effective in enhancing the productivity of different crops and suppressing the growth of various plant pathogens by producing antibacterial and anti-fungal compounds, hormones and siderophores. Application of vermiwash gave 60, 10, 26 and 27% higher yield in Knol khol (211.67qha-1), onion (177.81qha-1), French-bean (16.3qha-1 seed yield), Pea (16.3qha-1) and Paddy (28.45qha-1), respetively over control. Panchagavya 6 per cent spray recorded significantly higher Capsicum fruit yield (30.25, 37.49, 48.91, 118.91, 96.15, 86.29, 47.81 q ha-1 at 60, 70, 80, 90, 100, 110 and 120 DAT, respectively), N-fixers life (23.68, 25.59 at 60 DAT and 17.77, 17.18 X 103 at harvest during kharif and summer, respectively). Application of kunapajala (T-3) treatment was effective in enhancing the morphological parameters of the leaves of tomato plant followed by conventional farming (T-1) and organic farming (T-2).The beneficial microorganisms from Panchagavya and their establishment in the soil improves soil fertility and provide food grains free from the health hazards of using chemical fertilizers/ pesticides.Vermiwash, Beejamrit, and Jeevamirit as foliar were also proved quite effective in enhancing the productivity of different crops and effective against various plant pathogens.
***
A very important review on ecologically friendly and human friendly food that can be produced using traditional agricultural procedures developed over millennia of existence of agriculture.
A highly recommended contribution to all professionals who are open to new ideas. This review can serve as a recipe to discover approaches suitable to any country, climate, and conditions.
Thank you authors for providing us such great insight into this highly important part of our lives. We now know that good is defining the diversity and quality of our gut microbiota, which in turn defined our health. Your approach is gut microbiota friendly.
 
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Martin Kavšček, Martin Stražar, Tomaž Curk, Klaus Natter, and Uros Petrovic
Microbial Cell Factories 14(1):94 (June 2015)
DOI: 10.1186/s12934-015-0281-x
Abstract:
The yeast Saccharomyces cerevisiae is one of the oldest and most frequently used microorganisms in biotechnology with successful applications in the production of both bulk and fine chemicals. Yet, yeast researchers are faced with the challenge to further its transition from the old workhorse to a modern cell factory, fulfilling the requirements for next generation bioprocesses. Many of the principles and tools that are applied for this development originate from the field of synthetic biology and the engineered strains will indeed be synthetic organisms. We provide an overview of the most important aspects of this transition and highlight achievements in recent years as well as trends in which yeast currently lags behind. These aspects include: the enhancement of the substrate spectrum of yeast, with the focus on the efficient utilization of renewable feedstocks, the enhancement of the product spectrum through generation of independent circuits for the maintenance of redox balances and biosynthesis of common carbon building blocks, the requirement for accurate pathway control with improved genome editing and through orthogonal promoters , and improvement of the tolerance of yeast for specific stress conditions. The causative genetic elements for the required traits of the future yeast cell factories will be assembled into genetic modules for fast transfer between strains. These developments will benefit from progress in bio-computational methods, which allow for the integration of different kinds of data sets and algorithms, and from rapid advancement in genome editing, which will enable multiplexed targeted integration of whole heterologous pathways. The overall goal will be to provide a collection of modules and circuits that work independently and can be combined at will, depending on the individual conditions, and will result in an optimal synthetic host for a given production process.
***
This research on modification of living organisms demonstrates the capabilities and limits of the current scientific research on artificial life. Its consequences are manifold. Knowledge achieved here can be applied in medicine by finding novel treatments, can be applied in biocomputation (bio-computers), and finally show us the possible direction of development of military applications.
 
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Fan Zhang, Manhao Zeng, Ryan D. Yappert, Jiakai Sun, Yu-Hsuan Lee, Anne M. LaPointe, Baron Peters, Mahdi M. Abu-Omar, Susannah L. Scott
Science 370(6515) 437-441 (November 2020)
DOI: 10.1126/science.abc5441
Abstract
The current scale of plastics production and the accompanying waste disposal problems represent a largely untapped opportunity for chemical upcycling. Tandem catalytic conversion by platinum supported on γ-alumina converts various polyethylene grades in high yields (up to 80 weight percent) to low-molecular-weight liquid/wax products, in the absence of added solvent or molecular hydrogen, with little production of light gases. The major components are valuable long-chain alkylaromatics and alkylnaphthenes (average ~C30, dispersity Ð = 1.1). Coupling exothermic hydrogenolysis with endothermic aromatization renders the overall transformation thermodynamically accessible despite the moderate reaction temperature of 280°C. This approach demonstrates how waste polyolefins can be a viable feedstock for the generation of molecular hydrocarbon products.
Popularized version is here:
Video is here:
***
There are existing huge landfills full of PET. There had been developed a method of upcycling that dissolve used PET into a liquid form that can be reused with full functionality. This method is very promising form the ecological point of view.
 
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There was discovered a very simple, easy to made, no tools requiring way of water storage for high mountain areas that rely on water of thawing glaciers which become literally non-existent in many areas on Earth.
This and the following videos are nicely describing a fascinating environment friendly way of water storage. My admiration goes to the man who discovered this process. Thank you Sonam Wangchuk, Ladakh.
Another video:
Hopefully, we will find more such clever solutions like this that are highly environmentally friendly.
 
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Ryan K. Burdick, Juan Villabona, George A. Mashour, and Theodore Goodson
Scientific Reports 9(1) (August 2019)
DOI: 10.1038/s41598-019-47651-1
Abstract
Despite decades of research, the mechanism of anesthetic-induced unconsciousness remains incompletely understood, with some advocating for a quantum mechanical basis. Despite associations between general anesthesia and changes in physical properties such as electron spin, there has been no empirical demonstration that general anesthetics are capable of functional quantum interactions. In this work, we studied the linear and non-linear optical properties of the halogenated ethers sevoflurane (SEVO) and isoflurane (ISO), using UV-Vis spectroscopy, time dependent-density functional theory (TD-DFT) calculations, classical two-photon spectroscopy, and entangled two-photon spectroscopy. We show that both of these halogenated ethers interact with pairs of 800 nm entangled photons while neither interact with 800 nm classical photons. By contrast, nonhalogenated diethyl ether does not interact with entangled photons. This is the first experimental evidence that halogenated anesthetics can directly undergo quantum interaction mechanisms, offering a new approach to understanding their physicochemical properties.
***
This stream of research can open doors to the understanding of the true nature of consciousness. Our consciousness can be just light. Quantum mechanics is becoming a very useful tool in biomedical research.
 
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Vera Maura Fernandes de Lima and Wolfgang Hanke
Progress in Biophysics and Molecular Biology Dec 3:S0079-6107(20)30122-X (December 2020)
DOI: 10.1016/j.pbiomolbio.2020.11.002
Abstract
In this manuscript, we interpret the implications of a discovery we made in 1993 for the understanding of the spread of excitation waves in axon, central gray matter (isolated retina) and heart. We propose that the initial burst of energy dissipation in these waves measured as potentials drops, ionic activities marked changes or optical properties being mostly the effect of dissociated water becoming liquid water and be reversible due to the further on dissociation during the refractory period. We also propose experiments in order to falsify or agree with this conjecture.
***
Spread of excitation waves through excitable media is associated to changes of the water structure. A really interesting contribution is shown that paves our way towards better understanding of excitations in living organisms. Those observations deserve a greater attention within the whole scientific community.
 
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A.K. Choudhary, Saurabh Kumar, Rachana Dubey, Santosh Kumar and Abhay Kumar
International Web Conference on Global Research Initiatives for Sustainable Agriculture & Allied Sciences (GRISAAS-2020) during 28-30 December 2020
Introduction
The growing demand for organic products has been observed in recent years. US, Germany, France and China have emerged as big markets for organic products. Even in India, we have observed increasing demand for such products. To meet the growing demand the world over, organic farming has received further attention and impetus. This is evident from continued increase of acreages under organic farming, which is now practiced globally on more than 71 Mha of cultivable land. Although high input agriculture (conventional farming) has provided food security the world over, it has serious effects on human and soil health and environment. Conventionally produced foods have toxic levels of insecticides and herbicides; the residual presence of such chemicals has adversely affected the micro-flora and micro-fauna population in the soil. Moreover, conventional farming exerts tremendous pressure on natural resources (Aguilera et al., 2015). Contrary to this, organic farming can produce enough nutritious food to feed the world without disturbing the environment, while being more resilient to climate change and improving the livelihoods of farmers. Organic farming uses fewer pesticides, reduces soil erosion, decreases nitrate leaching into groundwater and surface water, and recycles animal wastes back into the farm (Goel et al., 2020). Besides this, organic farming uses less energy and generates fewer emissions while revitalizing the soil and sequestering carbon (Niemiec et al., 2020). Organic farming can outperform conventional farming under abiotic stresses like drought or flooding (Rajib et al., 2013). It is, therefore, imperative to assess the potential, constraints and prospects of organic farming as the sustainable and environmentally friendly approach to crop and food production.
 
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Rosaria Conte and Mario Paolucci
Front. Psychol. 5:668. (14 July 2014)
Abstract
In the first part of the paper, the field of agent-based modeling (ABM) is discussed focusing on the role of generative theories, aiming at explaining phenomena by growing them. After a brief analysis of the major strengths of the field some crucial weaknesses are analyzed. In particular, the generative power of ABM is found to have been underexploited, as the pressure for simple recipes has prevailed and shadowed the application of rich cognitive models. In the second part of the paper, the renewal of interest for Computational Social Science (CSS) is focused upon, and several of its variants, such as deductive, generative, and complex CSS, are identified and described. In the concluding remarks, an interdisciplinary variant, which takes after ABM, reconciling it with the quantitative one, is proposed as a fundamental requirement for a new program of the CSS.
***
Comments:
A must read review for everyone who wants to understand agent-based modeling of sociology, psychology, and beyond. All major pros and cons are discussed that makes this paper highly valuable and unique.
 
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Eugene Wigner
Communications in Pure and Applied Mathematics, vol. 13, No. I (February 1960). New York: John Wiley & Sons
Preamble -- quotation from another author:
Mathematics, rightly viewed, possesses not only truth, but supreme beautya beauty cold and austere, like that of sculpture, without appeal to any part of our weaker nature, without the gorgeous trappings of painting or music, yet sublimely pure, and capable of a stern perfection such as only the greatest art can show. The true spirit of delight, the exaltation, the sense of being more than Man, which is the touchstone of the highest excellence, is to be found in mathematics as surely as in poetry.
--BERTRAND RUSSELL, Study of Mathematics
From the text:
Naturally, we are inclined to smile about the simplicity of the classmate's approach. Nevertheless, when I heard this story, I had to admit to an eerie feeling because, surely, the reaction of the classmate betrayed only plain common sense. I was even more confused when, not many days later, someone came to me and expressed his bewilderment [1 The remark to be quoted was made by F. Werner when he was a student in Princeton.] with the fact that we make a rather narrow selection when choosing the data on which we test our theories. "How do we know that, if we made a theory which focuses its attention on phenomena we disregard and disregards some of the phenomena now commanding our attention, that we could not build another theory which has little in common with the present one but which, nevertheless, explains just as many phenomena as the present theory?" It has to be admitted that we have no definite evidence that there is no such theory.
Comments:
We all who are dealing with complex systems in biology and medicine must be aware of the foundations of all mathematical theories and their connection to the observations. Without this understanding there is not progress towards the future theories in biology. All theories are standing on a sort of quick sands.
 
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Sotiris Folinas and Theodore Metaxas
March 2020
DOI: 10.13140/RG.2.2.12069.24804
Abstract:
The purpose of this paper is to investigate the extent to which an epidemic such as 2019-nCoV can
affect the global tourism industry and the recording of the first estimates of the damage to world tourism. Countries such as China, where the epidemic began, but also Italy, where new cases are constantly being reported, are no longer tourist destinations. Potential tourists tend to postpone or cancel their plans for a destination that is plagued by a pandemic, especially when its main features are scarce of effective antivirus drugs and vaccines, the rapid spread of the virus and the damage that can cause to health (Reisinger & Mavondo, 2005). In cases of pandemics, tourists cancel their travels avoiding suspect places and people (Nicholl, 2006). Such kinds of pandemics affect directly industries such as tourism and retail service sector (Lee & McKibbin, 2004). The economic consequences of this outbreak will be serious and they will cause damages not only to the tourist destinations with an
important concentration of cases but also at a global level. A similar case is the outbreak of SARS in
2002 (Chou et al, 2003; Siu & Wong, 2003; Wen, 2003). Tourism is currently –March 2020- one of the most affected sectors and the World Tourism Organization has revised its 2020 forecast for international arrivals and receipts, though it emphasizes that such predictions are likely to be further revised (UNWTO, 2020). The United Nations specialized agency for tourism expects that international tourist arrivals will be down by 20% to 30% in 2020 when compared with 2019 figures. An expected fall of between 20-30% could translate into a decline in international tourism receipts (exports) of between US$300-450 billion, almost one-third of the US$ 1.5 trillion generated in 2019. Taking into account past market trends, this would mean that between five and seven years’ worth of growth will be lost to COVID-19 (UNWTO, 2020).
***
Comments:
The complexity of our world reached unpreceded levels. Any disruption of the system brings its substantial decrease of the effectivity. Generally, complex systems with their computational tools enable us to estimate the breaking point where the system undergoes a phase transition in the form of catastrophic failure.
 
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Hierarchical thermodynamics: a bit of history
Georgi Gladyshev
Method
October 2020
DOI: 10.13140/RG.2.2.22774.01607
Project: Hierarchical Thermodynamics - Foundation of Life
About: Everyone who wants to understand life must know its relationship to entropy, which describes the driving force of life. Names like father & son Carnot's, Gibbs, Boltzmann, Schroedinger, Turing, and von Neumann are paving our way towards an understanding of the very principles of life.
 
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Reka Zsuzsanna Albert and Albert-Laszlo Barabasi
Review of Modern Physics 74(1) (June 2001)
DOI: 10.1103/RevModPhys.74.47
Abstract:
Complex networks describe a wide range of systems in nature and society, much quoted examples including the cell, a network of chemicals linked by chemical reactions, or the Internet, a network of routers and computers connected by physical links. While traditionally these systems were modeled as random graphs, it is increasingly recognized that the topology and evolution of real networks is governed by robust organizing principles. Here we review the recent advances in the field of complex networks, focusing on the statistical mechanics of network topology and dynamics. After reviewing the empirical data that motivated the recent interest in networks, we discuss the main models and analytical tools, covering random graphs, small-world and scale-free networks, as well as the interplay between topology and the network's robustness against failures and attacks.
About:
Albert-Lazslo Barabasi is the founder of this research field: Complex Networks. I recommend to check out his Research Gate profile
or even better, his webpage
The book Linked is the way to dive into the field in a more accessible form. For sure it is possible to choose any of his papers -- earlier ones are easier to read -- and dive into this exciting field of research.
 
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Vito Marchitelli, Paolo Harabaglia, Claudia Troise, and Giuseppe De Natale
Scientific Reports volume 10, Article number: 11495 (July 2020)
Open access
Abstract:
Large earthquakes occurring worldwide have long been recognized to be non Poisson distributed, so involving some large scale correlation mechanism, which could be internal or external to the Earth. Till now, no statistically significant correlation of the global seismicity with one of the possible mechanisms has been demonstrated yet. In this paper, we analyze 20 years of proton density and velocity data, as recorded by the SOHO satellite, and the worldwide seismicity in the corresponding period, as reported by the ISC-GEM catalogue. We found clear correlation between proton density and the occurrence of large earthquakes (M > 5.6), with a time shift of one day. The significance of such correlation is very high, with probability to be wrong lower than 10–5. The correlation increases with the magnitude threshold of the seismic catalogue. A tentative model explaining such a correlation is also proposed, in terms of the reverse piezoelectric effect induced by the applied electric field related to the proton density. This result opens new perspectives in seismological interpretations, as well as in earthquake forecast.
***
Comments:
This observation can help governments to protect their entire populations against large scale disasters caused by earthquakes. Please share with all decision-makers, scientists, mayors, just everyone who can help to diminish the burden of societies due to those disasters.
 
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Stefan Valo
A forestry man who found the best solution to water evaporation from continents!
Words of Stefan Valo on Climate Error:
"A recent NASA study has proved that greenhouse gases are not the only culprit in causing global warming. There are also other causes we should not forget – such as landscape changing human activities. However, even in spite of this fact, lands as a factor influencing global warming and impacting overall climate change development in a negative way have been overlooked for a long time. In general, NASA points out mainly deforestation and the new farming methods as the activities with negative impact. Based on our observations and measurements, we indicate concrete causes behind climate change. But we are also presenting measures to remedy these causes. Both, the causes as well as the countermeasures, can be found under our feet."
The causes of water evaporation are
* Compressed soil
* Manmade slopes
More detailed information on easy & cheap solutions of these errors can be found on the webpage in English:
 
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Stefan Valo
"We are constantly speeding up water runoff from continents by draining the land via draining ditches, compressed surfaces, and broken pores in man-made slopes above roads. By doing this, we are draining and drying out the land, solar energy heats up the Earth's drained and dried surface. Subsequently, it is heating up the rising air, which is then retained in the Earth's atmosphere thanks to greenhouse gases."
"As a result, we can see. Global warming. Melting of glaciers and ice caps. Rising of ocean levels. Floods. Droughts. Lowering of river levels. Lowering of groundwater levels. Landslides. Drying of streams."
"The SOLUTION to all these EXISTS!"
Video:
***
Comments:
This is a very important message to all who want to stop the drying of the continents. All is experimentally proved and explained in the video.
 
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Robert Axelrod and Leigh Tesfatsion
Summary:
PURPOSE OF THE ON-LINE GUIDE
The purpose of this on-line guide is to suggest a short list of introductory readings and supporting materials to help newcomers become acquainted with Agent-Based Modeling (ABM).
Our primary intended audience is graduate students and advanced undergraduate students in the social sciences. However, researchers and teachers in a wide range of disciplines might also find the materials of use.
Unlike established methodologies such as statistics and mathematics, ABM has not yet developed a widely shared understanding of what a newcomer should learn. For decades, concepts such as the level of significance in statistics and the derivative in mathematics have been common knowledge that newcomers could be expected to learn. We hope that our selected readings and supporting materials will promote a shared understanding of ABM not only among newcomers to ABM but also among those who already use ABM.
Finally, a number of references below focus on a variant of ABM referred to as Agent-based Computational Economics (ACE). Roughly defined, ACE is the computational modeling of economic processes (including whole economies) as open-ended dynamic systems of interacting agents. A more formal characterization of ACE in terms of seven specific modeling principles is given at the ACE Homepage. These modeling principles help to distinguish ACE from standard economic modeling approaches as well as other forms of ABM.
 
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Castiello, U.
Journal of Comparative Psychology. Advance online publication. (2020).
Abstract
Up until the middle of the 19th century, some data about plant behavior could be found in books dealing with comparative psychology. The tendency gradually faded away, and the topic was almost exclusively treated in literature dealing with plant physiology. In recent years, however, there has been a revamping of psychological terminology and theorizing to describe, explain, and formulate hypotheses on the evidence that many of the sophisticated behaviors plants exhibit are an expression of cognitive competences that are generally attributed to human and nonhuman animals. In this work I shall discuss a selection of experimental studies supporting the idea that plants could be defined as cognitive agents. Experiments showing that the behavior of plants is controlled by a representation of its goal, episodic-like memory, and decision-making will be described. It is not, however, my intention to embrace any position as to whether or to what degree plants are conscious. Rather, I hope to (re)fuel the discussion within the psychological community that will point in the direction of integrating studies concerning adaptive plant behavior within the wider field of comparative psychology. (PsycInfo Database Record (c) 2020 APA, all rights reserved)
***
Comments of J.K.:
It always fascinated me, the ways of plant communication. We feel so superior to other living creatures but they have great, for us hidden, capabilities too.
 
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Jun Yang, Yu Yang, Weimin Wu, Jiao Zhao, Lei Jiang
Environmental Science and Technology 48(23) -- (November 2014)
DOI: 10.1021/es504038a
Abstract:
Polyethylene (PE) has been considered non-biodegradable for decades. Although the biodegradation of PE by bacterial cultures has been occasionally described, valid evidence of PE biodegradation has remained limited in the literature. We found that waxworms, or Indian mealmoths (the larvae of Plodia interpunctella), were capable of chewing and eating PE films. Two bacterial strains capable of degrading PE were isolated from this worm's gut, Enterobacter asburiae YT1 and Bacillus sp. YP1. Over a 28-day incubation period of the two strains on PE films, viable biofilms formed, and the PE films' hydrophobicity decreased. Obvious damage, including pits and cavities (0.3-0.4 µm in depth), was observed on the surfaces of the PE films using scanning electron microscopy (SEM) and atomic force microscopy (AFM). The formation of carbonyl groups was verified using X-ray photoelectron spectroscopy (XPS) and micro-attenuated total reflectance/Fourier transform infrared (micro-ATR/FTIR) imaging microscope. Suspension cultures of YT1 and YP1 (108 cells/ml) were able to degrade approximately 6.1  0.3% and 10.7  0.2% of the PE films (100 mg), respectively, over a 60-day incubation period. The molecular weights of the residual PE films were lower, and the release of 12 water-soluble daughter products was also detected. The results demonstrated the presence of PE-degrading bacteria in the guts of waxworms and provided promising evidence for the biodegradation of PE in the environment.
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Comments J.K.:
This can become an invaluable method in cleansing our ecosystems. Good to know. Good to share.
 
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Dan Styer
The Physics Teacher 57, 454 (2019);
Free PDF available.
[Correction: The Physics Teacher 58, 5 (2020)]
Abstract:
Before reading this essay, go to your kitchen and find a bottle of Italian salad dressing. Get one that’s been sitting still for a while at a fixed temperature—that is, one in thermal equilibrium. You’ll find an oil-rich layer at the top of the bottle and a vinegar-rich layer at the bottom (see Fig. 1). But think for a moment before spreading it over a delicious salad and eating up. That bottle’s in thermal equilibrium, so it’s in a state of maximum entropy. Doesn’t entropy mean “disorder”? No one would call a stack of 50 pennies and 50 dimes disordered if all the dimes were on the top and all the pennies at the bottom. So why is this salad dressing at thermal equilibrium segregated like an ordered stack of coins?
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Comments J.K.:
Everyone who wants to understand the roots of science cannot miss this fundamental concept buried down in foundations of science. Once you understand it, the whole scientific understanding becomes richer.
 
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Arieh Ben-Naim (The Hebrew University of Jerusalem, Israel)
July 2016
Pages: 276
About the book:
"It can be used as a supplementary material for teaching thermodynamics and statistical physics at an undergraduate or postgraduate level and can be a great read for undergraduate and postgraduate students of Sciences and Engineering."
Contemporary Physics
In this unique book, the reader is invited to experience the joy of appreciating something which has eluded understanding for many years — entropy and the Second Law of Thermodynamics. The book has a two-pronged message: first, that the Second Law is not infinitely incomprehensible as commonly stated in most textbooks on thermodynamics, but can, in fact, be comprehended through sheer common sense; and second, that entropy is not a mysterious quantity that has resisted understanding but a simple, familiar and easily comprehensible concept.
Written in an accessible style, the book guides the reader through an abundance of dice games and examples from everyday life. The author paves the way for readers to discover for themselves what entropy is, how it changes, and, most importantly, why it always changes in one direction in a spontaneous process.
In this new edition, seven simulated games are included so that the reader can actually experiment with the games described in the book. These simulated games are meant to enhance the readers' understanding and sense of joy upon discovering the Second Law of Thermodynamics.
All errors in the previous edition were corrected and a whole new section (7.7) has been added in which the meaning of entropy is explained in simple language.
Video intro on the Bestsellers on Entropy by Arieh Ben-Naim
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JK's comments:
Definitely the book you want to read when you need to know all about entropy but have no training in this specific area of physics. It is written in so clean and easy-to-follow form that it is the must-go book for all biologists and biomedical researchers.
It will open you yet unknown horizons in your own research. Nothing will look the same after reading this book.
 
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Author: Jake VanderPlas
2013
The software description page:
From the preamble:
In 1970 the British Mathematician John Conway created his "Game of Life" -- a set of rules that mimics the chaotic yet patterned growth of a colony of biological organisms. The "game" takes place on a two-dimensional grid consisting of "living" and "dead" cells, and the rules to step from generation to generation are simple:
* Overpopulation: if a living cell is surrounded by more than three living cells, it dies.
* Stasis: if a living cell is surrounded by two or three living cells, it survives.
* Underpopulation: if a living cell is surrounded by fewer than two living cells, it dies.
* Reproduction: if a dead cell is surrounded by exactly three cells, it becomes a live cell.
By enforcing these rules in sequential steps, beautiful and unexpected patterns can appear.
I was thinking about classic problems that could be used to demonstrate the effectiveness of Python for computing and visualizing dynamic phenomena, and thought back to a high school course I took where we had an assignment to implement a Game Of Life computation in C++. If only I'd had access to IPython and associated tools back then, my homework assignment would have been a whole lot easier!
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Comments:
When you love to play with things, you can use this code to start playing around with complex systems. The 'Game of Life' of John Conway is an ideal playground for any beginner in complexity as it is very easy to understand, yet it expresses endless possibilities and types of complex behavior.
The most amazing in this game is, of course, all kinds and sorts of emergent structures.
For professionals, it had been proven that GoL is a Turing machine equivalent. Shortly, it can compute all that is computable. Actually, we can build a whole computer using GoL. This is just fascinating :-)
 
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Hermann Haken
Book published in 1983
Springer-Verlag Berlin Heidelberg
Springer Series in Synergetics -- Series Volume 1
DOI 10.1007/978-3-642-88338-5
From the book cover:
Over the past years the field of synergetics has been mushrooming. An ever­ increasing number of scientific papers are published on the subject, and numerous conferences all over the world are devoted to it. Depending on the particular aspects of synergetics being treated, these conferences can have such varied titles as "Nonequilibrium Nonlinear Statistical Physics," "Self-Organization," "Chaos and Order," and others. Many professors and students have expressed the view that the present book provides a good introduction to this new field. This is also reflected by the fact that it has been translated into Russian, Japanese, Chinese, German, and other languages, and that the second edition has also sold out. I am taking the third edition as an opportunity to cover some important recent developments and to make the book still more readable. First, I have largely revised the section on self-organization in continuously extended media and entirely rewritten the section on the Benard instability. Sec­ond, because the methods of synergetics are penetrating such fields as eco­nomics, I have included an economic model on the transition from full employ­ meant to underemployment in which I use the concept of nonequilibrium phase transitions developed elsewhere in the book. Third, because a great many papers are currently devoted to the fascinating problem of chaotic motion, I have added a section on discrete maps. These maps are widely used in such problems and can reveal period-doubling bifurcations, intermittency, and chaos.
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Comments:
It has been decades when this book came through my hands. Actually it was 'through' my brain. I was studying this book without a pen/pencil and paper and carried out all derivations from my head.
It is a definitely excellently written account on synergetics based on ordinary and partial differential equations.
This book will help you smoothly transition from the classical mathematical approaches based on calculus towards modern ones based on massively parallel computational models.
One of the best-written books on the topic and simultaneously the best understandable book that I had ever read about the roots of complexity.
It should definitely become part of your internal library of tools and approaches used to solve problems.
 
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By Jordana Cepelewicz
Quanta Magazine -- May 13, 2020
Newly discovered worlds of microbes far beneath the ocean floor, inside old basaltic rocks, could point to a greater likelihood of life elsewhere in the universe.
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Comments:
Deep Biosphere: A popular description of a very exciting subject where we found deep located life -- up to kilometers under the surfaces -- thriving there without sun and living on energy that is stored in hydrogen atoms.
It points out that life could arise more than once on the Earth and similarly, it can arise anywhere in the universe where is the presence of volcanic rocks and water.
 
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Robert Johanson
April 16, 2016
Everyone who wants to achieve the capability of fast prototyping in scientific research while -- for example -- developing computational models, doing statistical analysis, performing machine learning, and much more is recommended to use the scientific programming language called Python.
The best way is to download the following PDF file defining the use of scientific Python and start to learn. It is not so difficult when C and CC+ knowledge is already present.
Later, the work can be recast into C++ whenever it is found to be important.
The link to the official PDF file:
An excerpt from the book:
Science has traditionally been divided into experimental and theoretical disciplines, but during the last several decades computing has emerged as a very important part of science. Scientific computing is often
closely related to theory, but it also has many characteristics in common with experimental work. It is
therefore often viewed as a new third branch of science. In most fields of science, computational work is an important complement to both experiments and theory, and nowadays a vast majority of both experimental and theoretical papers involve some numerical calculations, simulations or computer modeling.
In experimental and theoretical sciences there are well established codes of conducts for how results
and methods are published and made available to other scientists. For example, in theoretical sciences,
derivations, proofs and other results are published in full detail, or made available upon request. Likewise,
in experimental sciences, the methods used and the results are published, and all experimental data should
be available upon request. It is considered unscientific to withhold crucial details in a theoretical proof or
experimental method, that would hinder other scientists from replicating and reproducing the results.
In computational sciences there are not yet any well established guidelines for how source code and
generated data should be handled. For example, it is relatively rare that source code used in simulations for
published papers are provided to readers, in contrast to the open nature of experimental and theoretical work.
And it is not uncommon that source code for simulation software is withheld and considered a competitive advantage (or unnecessary to publish).
However, this issue has recently started to attract increasing attention, and a number of editorials in
high-profile journals have called for increased openness in computational sciences. Some prestigious journals, including Science, have even started to demand of authors to provide the source code for simulation software used in publications to readers upon request. Discussions are also ongoing on how to facilitate distribution of scientific software, for example as supplementary materials to scientific papers.
 
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Call it the Science Readiness Reserves—a group that will anticipate and prepare for rare but disastrous events such as pandemics, asteroid strikes, and more
The article in Scientific American exploring the necessity to create World Disater Scientific Board.
 
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Derek Groen, Robin A. Richardson, Rachel Coy, Ulf D. Schiller, Hoskote Chandrashekar, Fergus James Robertson, Peter V. Coveney
Frontiers in Physiology 9 (June 2018)
DOI: 10.3389/fphys.2018.00721
Abstract:
We present a validation study comparing results from a patient-specific lattice-Boltzmann simulation to transcranial Doppler (TCD) velocity measurements in four different planes of the middle cerebral artery (MCA). As part of the study, we compared simulations using a Newtonian and a Carreau-Yasuda rheology model. We also investigated the viability of using downscaled velocities to reduce the required resolution. Simulations with unscaled velocities predict the maximum flow velocity with an error of less than 9%, independent of the rheology model chosen. The accuracy of the simulation predictions worsens considerably when simulations are run at reduced velocity, as is for example the case when inflow velocities from healthy individuals are used on a vascular model of a stroke patient. Our results demonstrate the importance of using directly measured and patient-specific inflow velocities when simulating blood flow in MCAs. We conclude that localized TCD measurements together with predictive simulations can be used to obtain flow estimates with high fidelity over a larger region, and reduce the need for more invasive flow measurement procedures.
Comments:
Have you ever wonder, whether it is possible to get inside one's skull without actually opening it and assessing an aneurism there. Here it is. Using a unique combination of computational fluid flow techniques, CT and NMR scans enable us to assess the dangers of a given aneurysm stage.
That all leads to a decrease in the probability of premature operation, which is not without dangers, and too late operation that leads to the aneurysm rupture.
Not easy to go throw but definitely worth if it. This is the future of this type of disease therapy.
 
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Dirk Helbing and Alan Kirman
SSRN Electronic Journal
(January 2013)
DOI: 10.2139/ssrn.2292370
Abstract
In this paper we argue that if we want to find a more satisfactory approach to tackling the major socio-economic problems we are facing, we need to thoroughly rethink the basic assumptions of macroeconomics and financial theory. Making minor modifications to the standard models to remove “imperfections” is not enough, the whole framework needs to be revisited. Let us here enumerate some of the standard assumptions and postulates of economic theory. 1. An economy is an equilibrium system. In other words, it is a system in which all markets systematically clear at each point of time, but where the equilibrium may be perturbed, from time to time by exogenous shocks. 2. Selfish or greedy behaviour of individuals yields a result that is beneficial to society – a modern, widespread, but inaccurate reformulation of the principle of the “invisible hand”. 3. Individuals and companies decide rationally. By this it is meant that individuals optimize under the constraints they are facing and that their choices satisfy some standard consistency axioms. 4. The behaviour of all the agents together can be treated as corresponding to that of an average or representative individual. 5. When the financial sector is analysed, it is assumed that financial markets are efficient. Efficiency here means that all the relevant information concerning an asset is reflected in the price of that asset. 6. For financial markets it is assumed that they function better if their liquidity is greater. 7. In financial markets, the more connected the network of individuals and institutions the more it reduces risks and the more stable and robust is the system. Below, we discuss the fundamental problems with these assumptions and outline some of the policy implications of improved assumptions.
***
The research was sent to me by
https://www.researchgate.net/profile/Dragan_Komljenovic , who is doing research in this area of complexity?
Thank you for sharing this important information with us. Dirk Helbing is a leading researcher in modeling using agents within the fields of sociology, society, and economy.
The topics covered are vital in this turbulent period of time as COVID-19 infection is demonstrating evident fragility of the economic system. Really worth to read.
 
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Reka Albert and Albert-Laszlo Barabasi
Review of Modern Physics 74(1) (Jan 30, 2002)
DOI: 10.1103/RevModPhys.74.47
This is the seminal work in the Complex Networks, which is an inseparable part of the description of many natural phenomena. Biology, medicine, and societies are full of complex systems besides physics.
It is a must-read paper to everyone who wants to understand the complexity and its applications as deeply as possible and definitely a very valuable tool in every researcher's toolkit.
Abstract:
Complex networks describe a wide range of systems in nature and society. Frequently cited examples include the cell, a network of chemicals linked by chemical reactions, and the Internet, a network of routers and computers connected by physical links. While traditionally these systems have been modeled as random graphs, it is increasingly recognized that the topology and evolution of real networks are governed by robust organizing principles. This article reviews the recent advances in the field of complex networks, focusing on the statistical mechanics of network topology and dynamics. After reviewing the empirical data that motivated the recent interest in networks, the authors discuss the main models and analytical tools, covering random graphs, small-world and scale-free networks, the emerging theory of evolving networks, and the interplay between topology and the network’s robustness against failures and attacks.
 
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The publication aims to provide all who want to start to program their own massively parallel computational environments a comprehensive introduction into the thinking and design strategies behind it.
There is an existing relatively high activation barrier while trying to program the first massively parallel computational tools.
This publication is aiming into filling this gap and into lowering this initial barrier. Hence, the whole development cycle of the software is covered in three well-documented examples. In one case, there is available open-source software (DRX simulations), which enables anyone to go into the core and modify it to the author's own needs.
Good luck with your own programming and development of the complex systems models on various natural phenomena observed within many scientific disciplines.
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Jiří Kroc
added a research item
Cellular automaton models of complex systems (CSs) are gaining greater popularity; simultaneously, they have proven the capability to solve real scientific and engineering applications. To enable everybody a quick penetration into the core of this type of modeling, three real applications of cellular automaton models, including selected open source software codes, are studied: laser dynamics, dynamic recrystallization (DRX) and surface catalytic reactions. The paper is written in a way that it enables any researcher to reach the cutting edge knowledge of the design principles of cellular automata (CA) models of the observed phenomena in any scientific field. The whole sequence of design steps is demonstrated: definition of the model using topology and local (transition) rule of a cellular automaton, achieved results, comparison to real experiments, calibration, pathological observations, flow diagrams, software, and discussions. Additionally, the whole paper demonstrates the extreme expressiveness and flexibility of massively parallel computational approaches compared to other computational approaches. The paper consists of the introductory parts that are explaining CSs, self-organization and emergence, entropy, and CA. This allows readers to realize that there is a large variability in definitions and solutions of this class of models. >>> <<< (Remark: Open-source software included).
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Donella H. Meadows
Book - Chelsea Green Publishing (2008)
ISBN 9781603580557
The book that represents the pinnacle of the period of time in research approaches when dynamical systems transitioned into complex systems.
It is very important, easy to understand book that helps to quickly pass through this transition period and to achieve full understanding of the very foundations of complex system and why we developed them in the first place.
About Donella Meadows:
A woman whose pioneering work in the 1970s still makes front-page news, Donella Meadows was a scientist, author, teacher, and farmer widely considered ahead of her time. She was one of the world's foremost systems analysts and lead author of the influential Limits to Growth--the 1972 book on global trends in population, economics, and the environment that was translated into 28 languages and became an international bestseller. That book launched a worldwide debate on the earth's capacity to withstand constant human development and expansion. Twenty years later, she and co-authors Dennis Meadows and Jorgen Randers reported on their follow-up study in Beyond the Limits and a final revision of their research, Limits to Growth: The 30-Year Update, was published in 2004.
Reviews and Praise:
Publishers Weekly, Starred Review-
Just before her death, scientist, farmer and leading environmentalist Meadows (1941-2001) completed an updated, 30th anniversary edition of her influential 1972 environmental call to action, Limits to Growth, as well as a draft of this book, in which she explains the methodology-systems analysis-she used in her ground-breaking work, and how it can be implemented for large-scale and individual problem solving. With humorous and commonplace examples for difficult concepts such as a "reinforcing feedback loop," (the more one brother pushes, the more the other brother pushes back), negative feedback (as in thermostats), accounting for delayed response (like in maintaining store inventory), Meadows leads readers through the increasingly complex ways that feedback loops operate to create self-organizing systems, in nature ("from viruses to redwood trees") and human endeavor. Further, Meadows explicates methods for fixing systems that have gone haywire ("The world's leaders are correctly fixated on economic growth ...but they're pushing with all their might in the wrong direction"). An invaluable companion piece to Limits to Growth, this is also a useful standalone overview of systems-based problem solving, "a simple book about a complex world" graced by the wisdom of a profound thinker committed to "shaping a better future.
More Reviews and Praise
"When I read Thinking in Systems I am reminded of the enormity of the gap between systemic thinkers and policy makers. If this book helps narrow the gap, it will be Dana's greatest contribution."--Lester Brown, founder and President, Earth Policy Institute
"Dana Meadows' exposition in this book exhibits a degree of clarity and simplicity that can only be attained by one who profoundly and honestly understands the subject at hand--in this case systems modeling. Many thanks to Diana Wright for bringing this extra legacy from Dana to us."--Herman Daly, Professor, School of Public Policy, University of Maryland at College Park
"Reading Thinking in Systems evokes the wisdom and even the voice of Dana Meadows. We are reminded of how she was not only one of the great systems thinkers, but also one of our greatest teachers. This is modestly called a primer, and indeed it is, but unlike most books with that title, this one quickly takes one from the elementary into deep systems thinking about issues as critical today as they were when Dana wrote these words. The discussion of oil use and the interaction of its extraction pattern with economic decision making should be required reading for all energy policy makers and energy company executives (as well as all informed citizens in a democracy). The fisheries case reminds us of how little any government or private actor has done to grasp the importance of takeout flows in determining stocks when the input flows are not within our control. The commentary on economics and, yes the need to consider limits, is a clear systems statement that clarifies a great deal of discussion that goes back to The Limits to Growth.
It is remarkable that Dana is able to explain with such clarity such systems concepts of stocks, flows, feedback, time delays, resilience, bounded rationality, and system boundaries and to illustrate each one with multiple informative examples. Her statement that goals that optimize subsystems will sub optimize the functioning of the total system, is truly profound. As the book moves from the 'mechanics' of systems dynamics to Dana's more philosophical perspective, we are treated to her inherent belief in human values that consider the good of all, and how much more effective considering the needs of others is likely to be in solving larger, complex problems. The universe and our society may be very complex and operate in counterintuitive, non-liner fashion, but following the insights of this book and applying them will provide for far more effective solutions to the challenges of a 7 billion person planet than current incremental, linear responses by governments, corporations and individuals."--Bill Moomaw, Professor of International Environmental Policy at the Fletcher School, Tufts University
"In Dana Meadows's brilliantly integrative worldview, everything causes everything else; cause and effect loop back on themselves. She was the clearest thinker and writer co-creating the art and science of systems dynamics, and Thinking in Systems distills her lifetime of wisdom. This clear, fun-to-read synthesis will help diverse readers everywhere to grasp and harness how our complex world really works."--Amory B. Lovins, Chairman and Chief Scientist, Rocky Mountain Institute
"Dana Meadows taught a generation of students, friends, and colleagues the art and science of thinking beyond conventional boundaries. For her systems thinking included the expected things like recognizing patterns, connections, leverage points, feedback loops and also the human qualities of judgment, foresight, and kindness. She was a teacher with insight and heart. This long anticipated book, the distillation of her life's work, is a gem."--David Orr, Professor of Environmental Studies and Politics, Oberlin College
"The publication of Thinking in Systems is a landmark. To live sustainably on our planet, we must learn to understand human-environment interactions as complex systems marked by the impact of human actions, the prominence of nonlinear change, the importance of initial conditions, and the significance of emergent properties. Dana Meadows' final contribution is the best and most accessible introduction to this way of thinking we have. This book is destined to shape our understanding of socio-ecological systems in the years to come in much the same way that Silent Spring taught us to understand the nature of ecosystems in the 1960s and 1970s."--Oran R. Young, Professor, Donald Bren School of Environmental Science and Management at University of California, Santa Barbara
"Thinking in Systems is required reading for anyone hoping to run a successful company, community, or country. Learning how to think in systems is now part of change-agent literacy. And this is the best book of its kind."--Hunter Lovins, founder and President of Natural Capital Solutions and coauthor of Natural Capitalism: Creating the Next Industrial Revolution
"Dana Meadows was one of the smartest people I ever knew, able to figure out the sensible answer to almost any problem. This book explains how she thought, and hence is of immense value to those of us who often wonder what she'd make of some new problem. A classic."--Bill McKibben, author of Deep Economy
"An inspiring sequel to Dana Meadows' lifetime of seminal contributions to systems thinking, this highly accessible book should be read by everyone concerned with the world's future and how we can make it as good as it possibly can be."--Peter H. Raven, President, Missouri Botanical Garden
"Few matched Dana Meadows remarkable blend of eloquence and clarity in making systems thinking understandable. When Dana began her career, the field was esoteric and academic. Today it is the sine quo non for intelligent action in business and society. The publication of Meadows' previously unfinished manuscript is a gift for leaders of all sorts and at all levels."--Peter M. Senge, author of The Fifth Discipline and The Necessary Revolution
 
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Bert Hölldobler & Edward O. Wilson
Book -- Harvard University Press (1998)
ISBN 9780674485266
This is the very first book that kicked my much deeper interest in complex systems theory, self-organization, and emergent behavior without even knowing the terms. When I had read the book, I was already working in the field on one specific problem in the hot working of metals called dynamic recrystallization.
This book was absolutely resonating with my understanding and ideas that were emerging during my own research on and design of the software simulating the given phenomenon. I was imagining from the very beginning hot-worked metal tiny pieces as little 'creatures' than somehow interact with its surroundings.
Later, I did realize that with my CA models, I did enter the world of massively parallel computations. By reading this book, you can too!
Enjoy it and welcome to the filed of massively parallel computations with it's unique way of thinking!
J.K.
Reviews:
“Hölldobler and Wilson have carefully distilled more than 80 years of their combined personal research and thorough knowledge of the literature to produce a book that is both packed with ideas and information and a joy to read. The authors subtitled their book ‘A Story of Scientific Exploration’ and, like all good stories, it has a logical progression and sensible themes and is hard to put down.”—C. Ronald Carroll, American Scientist
“Beautifully written and illustrated… These fifteen chapters are a bustling but well-organized ant heap, full of wonders natural and intellectual.”—Philip Morrison, Scientific American
“Everyone should read Journey to the Ants; it is a book to read right through; I have done so twice so far. It brings back the joy of science and restores the sense of wonder, it is truly food for thought. For me it is a beloved book that will stay at my bedside.”—James E. Lovelock, Times Higher Education Supplement
 
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Authors --- Team of developers (listed below) & Mitchel Resnick who developed the original version.
Words from the development team:
StarLogo TNG is The Next Generation of StarLogo modeling and simulation software. While this version holds true to the premise of StarLogo as a tool to create and understand simulations of complex systems, it also brings with it several advances - 3D graphics and sound, a blocks-based programming interface, and keyboard input - that make it a great tool for programming educational video games.
Through TNG we hope to:
* Lower the barrier to entry for programming with a graphical interface where language elements are represented by colored blocks that fit together like puzzle pieces.
* Entice more young people into programming through tools that facilitate making games.
* Use 3D graphics to make more compelling and rich games and simulation models.
Home page:
Download:
The StarLogo TNG Team
StarLogo TNG is developed by the MIT Scheller Teacher Education Program. The design and development team has included:
* Lead StarLogo TNG Designers
Eric Klopfer and Andrew Begel
* Lead StarLogo TNG Developers
Corey McCaffrey, Daniel Wendel, Aidan Ho, Ricarose Roque, William Jacobs, David Blau, Adam Rosenfield, Viknash Samy, David Greenspan, Linda Ye, Joshua Thorp
* StarLogo TNG Developers
Radu Berinde, Aleksander Zlateski, Brett Warne, David Greenberg, John Jackman, Lawrie Gibson, Mike Matczynski, Mike Lin, Jane Lanyue, Lauren Clement, Peter Nga, Michael D'Ambrosio,YaaLirng Tu, Xudan Lily Liu, Dennis Ramdass, Xuancheng Shao
* Based on Designs By
Priscilla DelCastillo and Saeed Arida
* With Additional Help From
Elizabeth Kim, Han Xu, Robert Crowell, Anson Tsai, Chester Tse,
* Projects Developed by
Eric Rosenbaum, David Mendiola and Bianca Farrell
* 3-D Models Developed by
Colin Greenhill and David Blau
* Curricula Developed by
Hal Scheintaub and Wendy Huang
* With Support From
The MIT Scheller Teacher Education Program and The National Science Foundation
* Thanks To
Mitchel Resnick for his support and previous work on StarLogo
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An excellent educational tool capable to develop deep programming skills in agent-based modeling. It is a descendant of StarLogo developed by Mitchel Resnick.
Definitely, it is recommended to read in conjunction with the book
Turtles, Termites, and Traffic Jams: Explorations in Massively Parallel Microworlds
By Mitchel Resnick
The software is very easy to use. It can be applied in the education of ten years old kids. An excellent tool to develop a mathematical understanding of many observed natural phenomena.
 
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Steven Johnson
Book - Scribner (2002)
ISBN13: 9780684868769
This is a must read book for all who want to know more about complex systems and their avesome ability to self-organize and express emergent behaviour.
Enter the fascinating world of emergent structures, systems, and societies.
About the book:
In the tradition of Being Digital and The Tipping Point, Steven Johnson, acclaimed as a "cultural critic with a poet's heart" (The Village Voice), takes readers on an eye-opening journey through emergence theory and its applications.
A NEW YORK TIMES NOTABLE BOOK
A VOICE LITERARY SUPPLEMENT TOP 25 FAVORITE BOOKS OF THE YEAR
AN ESQUIRE MAGAZINE BEST BOOK OF THE YEAR
Explaining why the whole is sometimes smarter than the sum of its parts, Johnson presents surprising examples of feedback, self-organization, and adaptive learning. How does a lively neighborhood evolve out of a disconnected group of shopkeepers, bartenders, and real estate developers? How does a media event take on a life of its own? How will new software programs create an intelligent World Wide Web?
In the coming years, the power of self-organization -- coupled with the connective technology of the Internet -- will usher in a revolution every bit as significant as the introduction of electricity. Provocative and engaging, Emergence puts you on the front lines of this exciting upheaval in science and thought.
Excerpt:
Introduction: Here Comes Everybody!
In August of 2000, a Japanese scientist named Toshiyuki Nakagaki announced that he had trained an amoebalike organism called slime mold to find the shortest route through a maze. Nakagaki had placed the mold in a small maze comprising four possible routes and planted pieces of food at two of the exits. Despite its being an incredibly primitive organism (a close relative of ordinary fungi) with no centralized brain whatsoever, the slime mold managed to plot the most efficient route to the food, stretching its body through the maze so that it connected directly to the two food sources. Without any apparent cognitive resources, the slime mold had "solved" the maze puzzle.
For such a simple organism, the slime mold has an impressive intellectual pedigree. Nakagaki's announcement was only the latest in a long chain of investigations into the subtleties of slime mold behavior. For scientists trying to understand systems that use relatively simple components to build higher-level intelligence, the slime mold may someday be seen as the equivalent of the finches and tortoises that Darwin observed on the Galápagos Islands.
How did such a lowly organism come to play such an important scientific role? That story begins in the late sixties in New York City, with a scientist named Evelyn Fox Keller. A Harvard Ph.D. in physics, Keller had written her dissertation on molecular biology, and she had spent some time exploring the nascent field of "nonequilibrium thermodynamics," which in later years would come to be associated with complexity theory. By 1968, she was working as an associate at Sloan-Kettering in Manhattan, thinking about the application of mathematics to biological problems. Mathematics had played such a tremendous role in expanding our understanding of physics, Keller thought -- so perhaps it might also be useful for understanding living systems.
In the spring of 1968, Keller met a visiting scholar named Lee Segel, an applied mathematician who shared her interests. It was Segel who first introduced her to the bizarre conduct of the slime mold, and together they began a series of investigations that would help transform not just our understanding of biological development but also the disparate worlds of brain science, software design, and urban studies.
If you're reading these words during the summer in a suburban or rural part of the world, chances are somewhere near you a slime mold is growing. Walk through a normally cool, damp section of a forest on a dry and sunny day, or sift through the bark mulch that lies on a garden floor, and you may find a grotesque substance coating a few inches of rotting wood. On first inspection, the reddish orange mass suggests that the neighbor's dog has eaten something disagreeable, but if you observe the slime mold over several days -- or, even better, capture it with time-lapse photography -- you'll discover that it moves, ever so slowly, across the soil. If the weather conditions grow wetter and cooler, you may return to the same spot and find the creature has disappeared altogether. Has it wandered off to some other part of the forest? Or somehow vanished into thin air, like a puddle of water evaporating?
As it turns out, the slime mold (Dictyostelium discoideum) has done something far more mysterious, a trick of biology that had confounded scientists for centuries, before Keller and Segel began their collaboration. The slime mold behavior was so odd, in fact, that understanding it required thinking outside the boundaries of traditional disciplines -- which may be why it took a molecular biologist with a physics Ph.D.'s instincts to unravel the slime mold's mystery. For that is no disappearing act on the garden floor. The slime mold spends much of its life as thousands of distinct single-celled units, each moving separately from its other comrades. Under the right conditions, those myriad cells will coalesce again into a single, larger organism, which then begins its leisurely crawl across the garden floor, consuming rotting leaves and wood as it moves about. When the environment is less hospitable, the slime mold acts as a single organism; when the weather turns cooler and the mold enjoys a large food supply, "it" becomes a "they." The slime mold oscillates between being a single creature and a swarm.
While slime mold cells are relatively simple, they have attracted a disproportionate amount of attention from a number of different disciplines -- embryology, mathematics, computer science -- because they display such an intriguing example of coordinated group behavior. Anyone who has ever contemplated the great mystery of human physiology -- how do all my cells manage to work so well together? -- will find something resonant in the slime mold's swarm. If we could only figure out how the Dictyostelium pull it off, maybe we would gain some insight on our own baffling togetherness.
"I was at Sloan-Kettering in the biomath department -- and it was a very small department," Keller says today, laughing. While the field of mathematical biology was relatively new in the late sixties, it had a fascinating, if enigmatic, precedent in a then-little-known essay written by Alan Turing, the brilliant English code-breaker from World War II who also helped invent the digital computer. One of Turing's last published papers, before his death in 1954, had studied the riddle of "morphogenesis" -- the capacity of all life-forms to develop ever more baroque bodies out of impossibly simple beginnings. Turing's paper had focused more on the recurring numerical patterns of flowers, but it demonstrated using mathematical tools how a complex organism could assemble itself without any master planner calling the shots.
"I was thinking about slime mold aggregation as a model for thinking about development, and I came across Turing's paper," Keller says now, from her office at MIT. "And I thought: Bingo!"
For some time, researchers had understood that slime cells emitted a common substance called acrasin (also known as cyclic AMP), which was somehow involved in the aggregation process. But until Keller began her investigations, the conventional belief had been that slime mold swarms formed at the command of "pacemaker" cells that ordered the other cells to begin aggregating. In 1962, Harvard's B. M. Shafer showed how the pacemakers could use cyclic AMP as a signal of sorts to rally the troops; the slime mold generals would release the compounds at the appropriate moments, triggering waves of cyclic AMP that washed through the entire community, as each isolated cell relayed the signal to its neighbors. Slime mold aggregation, in effect, was a giant game of Telephone -- but only a few elite cells placed the original call.
It seemed like a perfectly reasonable explanation. We're naturally predisposed to think in terms of pacemakers, whether we're talking about fungi, political systems, or our own bodies. Our actions seem governed for the most part by the pacemaker cells in our brains, and for millennia we've built elaborate pacemakers cells into our social organizations, whether they come in the form of kings, dictators, or city councilmen. Much of the world around us can be explained in terms of command systems and hierarchies -- why should it be any different for the slime molds?
But Shafer's theory had one small problem: no one could find the pacemakers. While all observers agreed that waves of cyclic AMP did indeed flow through the slime mold community before aggregation, all the cells in the community were effectively interchangeable. None of them possessed any distinguishing characteristics that might elevate them to pacemaker status. Shafer's theory had presumed the existence of a cellular monarchy commanding the masses, but as it turned out, all slime mold cells were created equal.
For the twenty years that followed the publication of Shafer's original essay, mycologists assumed that the missing pacemaker cells were a sign of insufficient data, or poorly designed experiments: The generals were there somewhere in the mix, the scholars assumed -- they just didn't know what their uniforms looked like yet. But Keller and Segel took another, more radical approach. Turing's work on morphogenesis had sketched out a mathematical model wherein simple agents following simple rules could generate amazingly complex structures; perhaps the aggregations of slime mold cells were a real-world example of that behavior. Turing had focused primarily on the interactions between cells in a single organism, but it was perfectly reasonable to assume that the math would work for aggregations of free-floating cells. And so Keller started to think: What if Shafer had it wrong all along? What if the community of slime mold cells were organizing themselves? What if there were no pacemakers?
Keller and Segel's hunch paid off dramatically. While they lacked the advanced visualization tools of today's computers, the two scratched out a series of equations using pen and paper, equations that demonstrated how slime cells could trigger aggregation without following a leader, simply by altering the amount of cyclic AMP they released individually, then following trails of the pheromone that they encountered as they wandered through their environment. If the slime cells pumped out enough cyclic AMP, clusters of cells would start to form. Cells would begin following trails created by other cells, creating a positive feedback loop that encouraged more cells to join the cluster. If each solo cell was simply releasing cyclic AMP based on its own local assessment of the general conditions, Keller and Segel argued in a paper published in 1969, then the larger slime mold community might well be able to aggregate based on global changes in the environment -- all without a pacemaker cell calling the shots.
"The response was very interesting," Keller says now. "For anyone who understood applied mathematics, or had any experience in fluid dynamics, this was old hat to them. But to biologists, it didn't make any sense. I would give seminars to biologists, and they'd say, 'So? Where's the founder cell? Where's the pacemaker?' It didn't provide any satisfaction to them whatsoever." Indeed, the pacemaker hypothesis would continue as the reigning model for another decade, until a series of experiments convincingly proved that the slime mold cells were organizing from below. "It amazes me how difficult it is for people to think in terms of collective phenomenon," Keller says today.
Thirty years after the two researchers first sketched out their theory on paper, slime mold aggregation is now recognized as a classic case study in bottom-up behavior. Keller's colleague at MIT Mitch Resnick has even developed a computer simulation of slime mold cells aggregating, allowing students to explore the eerie, invisible hand of self-organization by altering the number of cells in the environment, and the levels of cyclic AMP distributed. First-time users of Resnick's simulation invariably say that the on-screen images -- brilliant clusters of red cells and green pheromone trails -- remind them of video games, and in fact the comparison reveals a secret lineage. Some of today's most popular computer games resemble slime mold cells because they are loosely based on the equations that Keller and Segel formulated by hand in the late sixties. We like to talk about life on earth evolving out of the primordial soup. We could just as easily say that the most interesting digital life on our computer screens today evolved out of the slime mold.
You can think of Segel and Keller's breakthrough as one of the first few stones to start tumbling at the outset of a landslide. Other stones were moving along with theirs -- some of whose trajectories we'll follow in the coming pages -- but that initial movement was nothing compared to the avalanche that followed over the next two decades. At the end of its course, that landslide had somehow conjured up a handful of fully credited scientific disciplines, a global network of research labs and think tanks, and an entire patois of buzzwords. Thirty years after Keller challenged the pacemaker hypothesis, students now take courses in "self-organization studies," and bottom-up software helps organize the Web's most lively virtual communities. But Keller's challenge did more than help trigger a series of intellectual trends. It also unearthed a secret history of decentralized thinking, a history that had been submerged for many years beneath the weight of the pacemaker hypothesis and the traditional boundaries of scientific research. People had been thinking about emergent behavior in all its diverse guises for centuries, if not millennia, but all that thinking had consistently been ignored as a unified body of work -- because there was nothing unified about its body. There were isolated cells pursuing the mysteries of emergence, but no aggregation.
Indeed, some of the great minds of the last few centuries -- Adam Smith, Friedrich Engels, Charles Darwin, Alan Turing -- contributed to the unknown science of self-organization, but because the science didn't exist yet as a recognized field, their work ended up being filed on more familiar shelves. From a certain angle, those taxonomies made sense, because the leading figures of this new discipline didn't even themselves realize that they were struggling to understand the laws of emergence. They were wrestling with local issues, in clearly defined fields: how ant colonies learn to forage and built nests; why industrial neighborhoods form along class lines; how our minds learn to recognize faces. You can answer all of these questions without resorting to the sciences of complexity and self-organization, but those answers all share a common pattern, as clear as the whorls of a fingerprint. But to see it as a pattern you needed to encounter it in several contexts. Only when the pattern was detected did people begin to think about studying self-organizing systems on their own merits. Keller and Segel saw it in the slime mold assemblages; Jane Jacobs saw it in the formation of city neighborhoods; Marvin Minsky in the distributed networks of the human brain.
What features do all these systems share? In the simplest terms, they solve problems by drawing on masses of relatively stupid elements, rather than a single, intelligent "executive branch." They are bottom-up systems, not top-down. They get their smarts from below. In a more technical language, they are complex adaptive systems that display emergent behavior. In these systems, agents residing on one scale start producing behavior that lies one scale above them: ants create colonies; urbanites create neighborhoods; simple pattern-recognition software learns how to recommend new books. The movement from low-level rules to higher-level sophistication is what we call emergence.
Imagine a billiard table populated by semi-intelligent, motorized billiard balls that have been programmed to explore the space of the table and alter their movement patterns based on specific interactions with other balls. For the most part, the table is in permanent motion, with balls colliding constantly, switching directions and speed every second. Because they are motorized, they never slow down unless their rules instruct them to, and their programming enables them to take unexpected turns when they encounter other balls. Such a system would define the most elemental form of complex behavior: a system with multiple agents dynamically interacting in multiple ways, following local rules and oblivious to any higher-level instructions. But it wouldn't truly be considered emergent until those local interactions resulted in some kind of discernible macrobehavior. Say the local rules of behavior followed by the balls ended up dividing the table into two clusters of even-numbered and odd-numbered balls. That would mark the beginnings of emergence, a higher-level pattern arising out of parallel complex interactions between local agents. The balls aren't programmed explicitly to cluster in two groups; they're programmed to follow much more random rules: swerve left when they collide with a solid-colored; accelerate after contact with the three ball; stop dead in their tracks when they hit the eight ball; and so on. Yet out of those low-level routines, a coherent shape emerges.
Does that make our mechanized billiard table adaptive? Not really, because a table divided between two clusters of balls is not terribly useful, either to the billiard balls themselves or to anyone else in the pool hall. But, like the proverbial Hamlet-writing monkeys, if we had an infinite number of tables in our pool hall, each following a different set of rules, one of those tables might randomly hit upon a rule set that would arrange all the balls in a perfect triangle, leaving the cue ball across the table ready for the break. That would be adaptive behavior in the larger ecosystem of the pool hall, assuming that it was in the interest of our billiards system to attract players. The system would use local rules between interacting agents to create higher-level behavior well suited to its environment.
Emergent complexity without adaptation is like the intricate crystals formed by a snowflake: it's a beautiful pattern, but it has no function. The forms of emergent behavior that we'll examine in this book show the distinctive quality of growing smarter over time, and of responding to the specific and changing needs of their environment. In that sense, most of the systems we'll look at are more dynamic than our adaptive billiards table: they rarely settle in on a single, frozen shape; they form patterns in time as well as space. A better example might be a table that self-organizes into a billiards-based timing device: with the cue ball bouncing off the eight ball sixty times a minute, and the remaining balls shifting from one side of the table to another every hour on the hour. That might sound like an unlikely system to emerge out of local interactions between individual balls, but your body contains numerous organic clocks built out of simple cells that function in remarkably similar ways. An infinite number of cellular or billiard-ball configurations will not produce a working clock, and only a tiny number will. So the question becomes, how do you push your emergent system toward clocklike behavior, if that's your goal? How do you make a self-organizing system more adaptive?
That question has become particularly crucial, because the history of emergence has entered a new phase in the past few years, one that should prove to be more revolutionary than the two phases before it. In the first phase, inquiring minds struggled to understand the forces of self-organization without realizing what they were up against. In the second, certain sectors of the scientific community began to see self-organization as a problem that transcended local disciplines and set out to solve that problem, partially by comparing behavior in one area to behavior in another. By watching the slime mold cells next to the ant colonies, you could see the shared behavior in ways that would have been unimaginable watching either on its own. Self-organization became an object of study in its own right, leading to the creation of celebrated research centers such as the Santa Fe Institute, which devoted itself to the study of complexity in all its diverse forms.
But in the third phase -- the one that began sometime in the past decade, the one that lies at the very heart of this book -- we stopped analyzing emergence and started creating it. We began building self-organizing systems into our software applications, our video games, our art, our music. We built emergent systems to recommend new books, recognize our voices, or find mates. For as long as complex organisms have been alive, they have lived under the laws of self-organization, but in recent years our day-to-day life has become overrun with artificial emergence: systems built with a conscious understanding of what emergence is, systems designed to exploit those laws the same way our nuclear reactors exploit the laws of atomic physics. Up to now, the philosophers of emergence have struggled to interpret the world. But they are now starting to change it.
What follows is a tour of fields that aren't usually gathered between the same book jacket covers. We'll look at computer games that simulate living ecologies; the guild system of twelfth-century Florence; the initial cell divisions that mark the very beginning of life; and software that lets you see the patterns of your own brain. What unites these different phenomena is a recurring pattern and shape: a network of self-organization, of disparate agents that unwittingly create a higher-level order. At each scale, you can see the imprint of those slime mold cells converging; at each scale, the laws of emergence hold true.
This book roughly follows the chronology of the three historical phases. The first section introduces one of the emergent world's crowning achievements -- the colony behavior of social insects such as ants and termites -- and then goes back to trace part of the history of the decentralized mind-set, from Engels on the streets of Manchester to the new forms of emergent software being developed today. The second section is an overview of emergence as we currently understand it; each of the four chapters in the section explores one of the field's core principles: neighbor interaction, pattern recognition, feedback, and indirect control. The final section looks to the future of artificial emergence and speculates on what will happen when our media experiences and political movements are largely shaped by bottom-up forces, and not top-down ones.
Certain shapes and patterns hover over different moments in time, haunting and inspiring the individuals living through those periods. The epic clash and subsequent resolution of the dialectic animated the first half of the nineteenth century; the Darwinian and social reform movements scattered web imagery through the second half of the century. The first few decades of the twentieth century found their ultimate expression in the exuberant anarchy of the explosion, while later decades lost themselves in the faceless regimen of the grid. You can see the last ten years or so as a return to those Victorian webs, though I suspect the image that has been burned into our retinas over the past decade is more prosaic: windows piled atop one another on a screen, or perhaps a mouse clicking on an icon.
These shapes are shorthand for a moment in time, a way of evoking an era and its peculiar obsessions. For individuals living within these periods, the shapes are cognitive building blocks, tools for thought: Charles Darwin and George Eliot used the web as a way of understanding biological evolution and social struggles; a half century later, the futurists embraced the explosions of machine-gun fire, while Picasso used them to re-create the horrors of war in Guernica. The shapes are a way of interpreting the world, and while no shape completely represents its epoch, they are an undeniable component of the history of thinking.
When I imagine the shape that will hover above the first half of the twenty-first century, what comes to mind is not the coiled embrace of the genome, or the etched latticework of the silicon chip. It is instead the pulsing red and green pixels of Mitch Resnick's slime mold simulation, moving erratically across the screen at first, then slowly coalescing into larger forms. The shape of those clusters -- with their lifelike irregularity, and their absent pacemakers -- is the shape that will define the coming decades. I see them on the screen, growing and dividing, and I think: That way lies the future.
Copyright &copy; 2001 by Steven Johnson
 
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Andrew Ilachinski
(Center for Naval Analyses, USA)
Book - World Scientific (2004)
DOI 10.1142/5531
From the book cover:
Military conflicts, particularly land combat, possess the characteristics of complex adaptive systems: combat forces are composed of a large number of nonlinearly interacting parts and are organized in a dynamic command-and-control network; local action, which often appears disordered, self-organizes into long-range order; military conflicts, by their nature, proceed far from equilibrium; military forces adapt to a changing combat environment; and there is no master “voice” that dictates the actions of every soldier (i.e., battlefield action is decentralized). Nonetheless, most modern “state of the art” military simulations ignore the self-organizing properties of combat.
This book summarizes the results of a multiyear research effort aimed at exploring the applicability of complex adaptive systems theory to the study of warfare, and introduces a sophisticated multiagent-based simulation of combat called EINSTein. EINSTein, whose bottom-up, generative approach to modeling combat stands in stark contrast to the top-down or reductionist philosophy that still underlies most conventional military models, is designed to illustrate how many aspects of land combat may be understood as self-organized, emergent phenomena. Used worldwide by the military operations research community, EINSTein has pioneered the simulation of combat on a small to medium scale by using autonomous agents to model individual behaviors and personalities rather than hardware.
Contents:
Nonlinear Dynamics, Deterministic Chaos, and Complex Adaptive Systems: A Primer
Nonlinearity, Complexity, and Warfare: Eight Tiers of Applicability
EINSTein: Mathematical Overview
EINSTein: Methodology
EINSTein: Sample Behavior
Breeding Agents
Concluding Remarks and Speculations
Readership: Undergraduates, graduate students, academics and researchers in computer science; political and physical scientists; computer game developers; military historians.
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Everyone who wants to understand the core of agent-based modeling will greatly benefit from reading and understanding the topics covered in this book.
Readers will enter the fascinating world of agents that self-organize themselves into certain patterns in space and time.
This book is opening doors to an understanding of many other biological phenomena that are observed on many structural levels of biological systems: biomolecules, cellular building blocks, cells, tissues, organs, entities, societies, and ecosystems.
The book is unique because it describes the principles of programs and the resulting behavior in the same place! A very good introduction prior to starting to program an own agent-based system or when using some commercial or open-source code.
 
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Per Bak
Book - Copernicus (1996)
DOI 10.1007/978-1-4757-5426-1
From the book cover
... and acknowledgments Self-organized criticality is a new way of viewing nature. The basic picture is one where nature is perpetually out of balance, but organized in a poised state-the critical state-where anything can happen within well-defined statistical laws. The aim of the science of self-organized criticality is to yield insight into the fundamental question of why nature is complex, not simple, as the laws of physics imply. Self-organized criticality explains some ubiquitous patterns existing in nature that we view as complex. Fractal structure and catastrophic events are among those regularities. Applications range from the study of pulsars and black holes to earthquakes and the evolution of life. One intriguing consequence of the theory is that catastrophes can occur for no reason whatsoever. Mass extinctions may take place without any external triggering mechanism such as a volcanic eruption or a meteorite hitting the earth (although the theory of course cannot rule out that this has in fact occurred). How Nature Works Since we first proposed the idea in 1987, more than 2, 000 papers have been written on self-organized criticality, making ours the most cited paper in physics during that period. How Nature Works is the first book to deal with the subject. The basic idea is simple, and most of the mathematical models that have been used in the implementation of the theory are not complicated.
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An interesting review covering the basics
 
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Per Bak, Chao Tang, Kurt Wiesenfeld
Physical Review Letters 59(4):381-384 (August 1987)
DOI: 10.1103/PhysRevLett.59.381
Abstract
We show that dynamical systems with spatial degrees of freedom naturally evolve into a self-organized critical point. Flicker noise, or 1/f noise, can be identified with the dynamics of the critical state. This picture also yields insight into the origin of fractal objects.
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Everyone who wants to understand the evolution of our understanding of complex systems and one of the key building blocks of it should study this research paper.
It covers the way by which self-organization and self-organized critically operates in the natural phenomena. It substantially changed our understanding of many phenomena observed but up-to-this-publication not understood.
Very crudely explained, the paper describes the systems which are fed by energy continuously but the release of this energy operates in the form of avalanches. With this model, we suddenly got a tool capable to describe many naturally observed phenomena: earthquakes, volcano eruptions, star activities, avalanches, landslides, and many others.
 
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Kai Nagel & Michael Schreckenberg
Journal de Physique I 2:2221(December 1992)
Abstract:
We introduce a stochastic discrete automaton model to freeway traffic. Monte-Carlo simulations of the model show a transition from laminar traffic flow to start-stop-waves with increasing vehicle density, as is observed in real freeway traffic. For special cases analytical results can be obtained.
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A model that explained--using a very simple stochastic cellular automata model--the causes of spontaneous occurrence of traffic flow jams on German highways even in the situations when the traffic was not too dense/heavy.
The traffic flow model is undergoing spontaneous phase transitions with dependence on the density of traffic flow exactly as observed.
It is the very first model of its kind--not only in traffic flow modeling. It described the distribution of traffic jams with respect to the intensity of traffic flow theoretically. It was and still is a great achievement.
Everyone who wants to understand self-organization, self-organized criticality, emergence, cellular automata & massive parallel modeling and design of models and other building block of complex systems modeling must know this model by the heart.
 
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This review aims mainly to all professionals from the fields of clinical medicine, biomedical and experimental research. It targets to deliver a quick starting overview and basic understanding of Complex Systems (CSs) with a citation apparatus enabling to efficiently reach the cutting-edge knowledge and applications. This paper has two main objectives. It builds the core information of CSs that is explained on a carefully selected example called the "Game of Life", which expresses self-organization and emergence. The second and most important objective is to provide a wide list of CSs computational methods enabling everybody to achieve a basic overview of all major methods applied in experimental and clinical medicine. These methods are easy to implement in any field of the interest.
Jiří Kroc
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