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Ecological communities by design

In synthetic ecology, a nascent offshoot of synthetic biology, scientists aim to design and construct microbial communities with desirable properties. Such mixed populations of microorganisms can simultaneously perform otherwise incompatible functions (1). Compared with individual organisms, they can also better resist losses in function as a result of environmental perturbation or invasion by other species (2). Synthetic ecology may thus be a promising approach for developing robust, stable biotechnological processes, such as the conversion of cellulosic biomass to biofuels (3). However, achieving this will require detailed knowledge of the principles that guide the structure and function of microbial communities (see the image).


Ecological communities by design
James K. Fredrickson

Science 26 June 2015:
Vol. 348 no. 6242 pp. 1425-1427
http://dx.doi.org/10.1126/science.aab0946

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Exogenous Rewards for Promoting Cooperation in Scale-Free Networks

The design of mechanisms that encourage pro-social behaviours in populations of self-regarding agents is recognised as a major theoretical challenge within several areas of social, life and engineering sciences. When interference from external parties is considered, several heuristics have been identified as capable of engineering a desired collective behaviour at a minimal cost. However, these studies neglect the diverse nature of contexts and social structures that characterise real-world populations. Here we analyse the impact of diversity by means of scale-free interaction networks with high and low levels of clustering, and test various interference mechanisms using simulations of agents facing a cooperative dilemma. Our results show that interference on scale-free networks is not trivial and that distinct levels of clustering react differently to each interference mechanism. As such, we argue that no tailored response fits all scale-free networks and present which mechanisms are more efficient at fostering cooperation in both types of networks. Finally, we discuss the pitfalls of considering reckless interference mechanisms.

 

Exogenous Rewards for Promoting Cooperation in Scale-Free Networks

Theodor Cimpeanu, The Anh Han, Francisco C. Santos

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Don’t let industry write the rules for AI

Don’t let industry write the rules for AI | Papers | Scoop.it

Companies’ input in shaping the future of AI is essential, but they cannot retain the power they have gained to frame research on how their systems impact society or on how we evaluate the effect morally. Governments and publicly accountable entities must support independent research, and insist that industry shares enough data for it to be kept accountable.

 

Don’t let industry write the rules for AI

 Yochai Benkler

Nature 569, 161 (2019)

doi: 10.1038/d41586-019-01413-1

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There Are No Laws of Physics. There’s Only the Landscape.

There Are No Laws of Physics. There’s Only the Landscape. | Papers | Scoop.it

Scientists seek a single description of reality. But modern physics allows for many different descriptions, many equivalent to one another, connected through a vast landscape of mathematical possibility.

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The Mind of Leonardo Da Vinci

The Mind of Leonardo Da Vinci | Papers | Scoop.it
Leonardo’s thinking was interdisciplinary. When he injected wax into the brain or into the heart to make casts of the inner workings of the body, he was borrowing the “lost wax” technique familiar to sculptors. When he studied friction and invented roller bearings and ball bearings he reasoned that frictional resistance differs according to the nature of the surfaces in contact, and increases in direct proportion to load, and he even estimated (for the first time) a coefficient of friction. But he went further to realize its relevance not just to machines but to the movements of tendons over bones; to the creation of heat by the heart; and to the production of voice by the friction of air on the vocal cords.
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Social alliances improve rank and fitness in convention-based societies

Social alliances improve rank and fitness in convention-based societies | Papers | Scoop.it

What forces produce and maintain social inequality, and why do society members tolerate this inequality? The “One Percent” clearly benefit from having high status, but low-status individuals have strong incentive to challenge the established pecking order and try to improve their position. This conundrum is particularly striking in the societies of many primates and spotted hyenas, where females who are born to low-status mothers rarely manage to improve their position. Here we find that females who are strongly allied with their group-mates are more likely to improve their status, and that upward social mobility is often achieved with support from their closest allies. This suggests that, much like some animals compete physically for status, these species compete through social alliances.

 

Social alliances improve rank and fitness in convention-based societies

Eli D. Strauss and Kay E. Holekamp
PNAS April 30, 2019 116 (18) 8919-8924

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Singularity cities

We propose an upgraded gravitational model which provides population counts beyond the binary (urban/non-urban) city simulations. Numerically studying the model output, we find that the radial population density gradients follow power-laws where the exponent is related to the preset gravity exponent γ. Similarly, the urban fraction decays exponentially, again determined by γ. The population density gradient can be related to radial fractality and it turns out that the typical exponents imply that cities are basically zero-dimensional. Increasing the gravity exponent leads to extreme compactness and the loss of radial symmetry. We study the shape of the major central cluster by means of another three fractal dimensions and find that overall its fractality is dominated by the size and the influence of γ is minor. The fundamental allometry, between population and area of the major central cluster, is related to the gravity exponent but restricted to the case of higher densities in large cities. We argue that cities are shaped by power-law proximity. We complement the numerical analysis by economics arguments employing travel costs as well as housing rent determined by supply and demand. Our work contributes to the understanding of gravitational effects, radial gradients, and urban morphology. The model allows to generate and investigate city structures under laboratory conditions.

 

Singularity cities
Yunfei Li, Diego Rybski, Jürgen P. Kropp

Environment and Planning B: Urban Analytics and City Science

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Particle velocity controls phase transitions in contagion dynamics

Particle velocity controls phase transitions in contagion dynamics | Papers | Scoop.it

Interactions often require the proximity between particles. The movement of particles, thus, drives the change of the neighbors which are located in their proximity, leading to a sequence of interactions. In pathogenic contagion, infections occur through proximal interactions, but at the same time, the movement facilitates the co-location of different strains. We analyze how the particle velocity impacts on the phase transitions on the contagion process of both a single infection and two cooperative infections. First, we identify an optimal velocity (close to half of the interaction range normalized by the recovery time) associated with the largest epidemic threshold, such that decreasing the velocity below the optimal value leads to larger outbreaks. Second, in the cooperative case, the system displays a continuous transition for low velocities, which becomes discontinuous for velocities of the order of three times the optimal velocity. Finally, we describe these characteristic regimes and explain the mechanisms driving the dynamics.

 

Particle velocity controls phase transitions in contagion dynamics
Jorge P. Rodríguez, Fakhteh Ghanbarnejad & Víctor M. Eguíluz
Scientific Reports volume 9, Article number: 6463 (2019)

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The necessity of extended autopoiesis

The theory of autopoiesis holds that an organism can be defined as a network of processes. However, an organism also has a physical body. The relationship between these two things—network and body—has been raised in this issue of Adaptive Behaviour, with reference to an extended interpretation of autopoiesis. This perspective holds that the network and the body are distinct things, and that the network should be thought of as extending beyond the boundaries of the body. The relationship between body and network is subtle, and I revisit it here from the extended perspective. I conclude that from an organism = network perspective, the body is a biological solution to the problem of maintaining both the distinctness of an organism, separate from but engaged with its environment and other organisms, and its distinctiveness as a particular individual.

 

The necessity of extended autopoiesis
Nathaniel Virgo
Adaptive Behavior

https://doi.org/10.1177/1059712319841557

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How Efficiency Shapes Human Language

We review recent research on the burgeoning topic of how language structure is shaped by principles of efficiency for communication and learning.
Work in this area has infused long-standing ideas in linguistics and psychology with new precision and methodological rigor by bringing together information theory, newly available datasets, controlled experimentation, and computational modeling.
We review a number of studies that focus on phenomena ranging from the lexicon through syntactic processes, and which deploy formal tools from information theory and probability theory to understand how and why language works the way that it does.
These studies show how a pervasive pressure for efficient usage guides the form of natural language and suggest a rich future for language research in connecting linguistics to cognitive psychology and mathematical theories of communication.

 

How Efficiency Shapes Human Language

Edward Gibson, et al.

Trends in Cognitive Science

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Information as a construction

The purpose of this review paper is to outline the constructivist approach to the notion of information from two perspectives. The first perspective explores the role of ‘constructed’ information in the ‘constructivist niche’ – a common name for the appropriate viewpoints in different science fields, such as cognitive and neuroscience, psychology, cybernetics and biology of cognition. The second perspective considers library and information science (LIS) papers in which information is treated as a constructed entity. This paper assumed the origin of the notion of information to be a construction as defined in the ‘constructivist niche’ that is based upon communication theory and cybernetics. Conversely, the origin of the notion of information as a construction as per LIS can be found in Bateson’s definition of information as a ‘difference which makes the difference,‘ as well as in the 1970s LIS definition wherein information is associated with the direction of a cognitive viewpoint, as in a ‘cognitive turn’. The study showed that ‘information as a construction‘, except in a few cases, did not play a significant role in the constructivist theories nor in LIS. LIS researchers reduce the concept of information to a subjective, socially-constructed entity which inherently results in different interpretations.

 

Information as a construction
Boris Bosancic, Marta Matijevic

Journal of Librarianship and Information Science

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Network properties of salmonella epidemics

Network properties of salmonella epidemics | Papers | Scoop.it

We examine non-typhoidal Salmonella (S. Typhimurium or STM) epidemics as complex systems, driven by evolution and interactions of diverse microbial strains, and focus on emergence of successful strains. Our findings challenge the established view that seasonal epidemics are associated with random sets of co-circulating STM genotypes. We use high-resolution molecular genotyping data comprising 17,107 STM isolates representing nine consecutive seasonal epidemics in Australia, genotyped by multiple-locus variable-number tandem-repeats analysis (MLVA). From these data, we infer weighted undirected networks based on distances between the MLVA profiles, depicting epidemics as networks of individual bacterial strains. The network analysis demonstrated dichotomy in STM populations which split into two distinct genetic branches, with markedly different prevalences. This distinction revealed the emergence of dominant STM strains defined by their local network topological properties, such as centrality, while correlating the development of new epidemics with global network features, such as small-world propensity.

 

Network properties of salmonella epidemics
Oliver M. Cliff, Vitali Sintchenko, Tania C. Sorrell, Kiranmayi Vadlamudi, Natalia McLean & Mikhail Prokopenko
Scientific Reports volume 9, Article number: 6159 (2019)

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Space: The Final Illusion

Space: The Final Illusion | Papers | Scoop.it

(...)  the takeaway lesson is that the intuitive idea that objects influence each other because they are close in space is soon to become another of those easy beliefs that turn out to be wrong when we look deeper. The smoothness of space is soon to become an illusion that hides a tiny and complex world of causal interactions, which do not live in space—but which rather define and create space as they create the future from the present.

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Temporal and spatial analysis of the media spotlight

  • An earthquake in Mexico received the spotlight of the media for several weeks, allowed quantifying media coverage.
  • A person from a large city receives more attention from the media, per person, than a person from a small city.
  • The coverage that the media places on a specific event or topic has an exponential decay. The coverage given to an event drops by half every eight days.

 

Temporal and spatial analysis of the media spotlight

Rafael Prieto Curiel, Carmen Cabrera Arnau, MaraTorres Pinedo, Humberto González Ramírez, Steven R.Bishop

Computers, Environment and Urban Systems
Volume 75, May 2019, Pages 254-263

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A map is not the territory, or is it?

‘A map is not the territory’ is a mantra introduced by the Polish-American mathematician Alfred Korzybski in an essay on the meaning of representation which he published in 1931. In it, he makes the very obvious point that an abstraction of something is not the thing itself and he uses the concept of the map to enforce this point. We all know what a map is. It is picture of the territory but with many details, in fact most details omitted. It may be similar to the thing but it can never be same. Korzybski’s thesis is a closely argued treatise about how close a representation must be to the thing it is associated with and in grappling with this problem, he implicitly defines a model, echoing to an extent the concept of the ‘digital twin’ that is preoccupying us somewhat in contemporary discussion of how we should build and use simulation models. In a previous editorial last year (Batty, 2018), I introduced the problem where I argued that such a digital twin must be an abstraction from the thing itself to which it is twinned. It may approach the thing itself but it can never be the same for the twin is a model as defined by an abstraction. Tomko and Winter (2019) took me to task in a rather gentle way for blurring this distinction in my saying that a twin is not the real thing but implying the twin needs to get as close as possible to the real thing. If we do get close, then the abstraction and the thing itself begin to merge. This does not quite reach the point where the twin is absorbed with the thing being abstracted but it does suggest that as our world – whether it be societies, cities, building complexes, etc. – evolves, then the digital landscape which hitherto we have regarded as something rather separate from the actual landscape begin to merge, producing a new landscape that is a mixture of both. We will elaborate this point below for it is intrinsic to the way in which material and digital societies relate to one another.

 

A map is not the territory, or is it?
Michael Batty
Environment and Planning B: Urban Analytics and City Science

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Can scientific productivity impact the economic complexity of countries?

The so-called index of economic complexity, based on nations’ exports, was initially proposed as an alternative to traditional macroeconomic metrics just as the scientific productivity of countries which has also been deemed as a better predictor of economic growth. Adequate scrutiny to the relationship between these two factors, however, remains little explored. This paper aims to examine the relationship between economic complexity and scientific production while identifying which areas of knowledge hold to this relationship best. By applying panel data techniques to a sample of 91 countries between 2003 and 2014, we found that scientific productivity in basic sciences and engineering has a significant positive effect on the economic complexity of countries. This relationship, however, only remains stable for high-income countries, where university-industry-government capabilities interact to stimulate and generate innovation and strategies for economic growth of firms.

 

Can scientific productivity impact the economic complexity of countries?

Henry Laverde-Rojas & Juan C. Correa

Scientometrics
pp 1–16

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Physicists Aim to Classify All Possible Phases of Matter

Physicists Aim to Classify All Possible Phases of Matter | Papers | Scoop.it

Led by dozens of top theorists, with input from mathematicians, researchers have already classified a huge swath of phases that can arise in one or two spatial dimensions by relating them to topology: the math that describes invariant properties of shapes like the sphere and the torus. They’ve also begun to explore the wilderness of phases that can arise near absolute zero in 3-D matter.

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Productivity, prominence, and the effects of academic environment

Past studies have shown that faculty at prestigious universities tend to be more productive and prominent than faculty at less prestigious universities. This pattern is usually attributed to a competitive job market that selects inherently productive faculty into prestigious positions. Here, we test the extent to which, instead, faculty’s work environments drive their productivity. Using comprehensive data on an entire field of research, we use a matched-pair experimental design to isolate the effects of training at, versus working in, prestigious environments. We find that faculty’s work environments, not selection effects, drive their productivity and prominence, establishing that where a researcher works serves as a mechanism for cumulative advantage, locking in past success via job placement and thereby facilitating future success.

Productivity, prominence, and the effects of academic environment

Samuel F. Way, Allison C. Morgan, Daniel B. Larremore, and Aaron Clauset
PNAS

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Evolution of empathetic moral evaluation

Social norms can promote cooperation by assigning reputations to individuals based on their past actions. A good reputation indicates that an individual is likely to reciprocate. A large body of research has established norms of moral assessment that promote cooperation, assuming reputations are objective. But without a centralized institution to provide objective evaluation, opinions about an individual’s reputation may differ across a population. In this setting we study the role of empathy–the capacity to form moral evaluations from another person’s perspective. We show that empathy tends to foster cooperation by reducing the rate of unjustified defection. The norms of moral evaluation previously considered most socially beneficial depend on high levels of empathy, whereas different norms maximize social welfare in populations incapable of empathy. Finally, we show that empathy itself can evolve through social contagion. We conclude that a capacity for empathy is a key component for sustaining cooperation in societies.

 

Evolution of empathetic moral evaluation
Arunas L Radzvilavicius, Alexander J Stewart, Joshua B Plotkin

eLife 2019;8:e44269 DOI: 10.7554/eLife.44269

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Complex Systems in Aesthetics and Arts

The arts are one of the most complex of human endeavours, and so it is fitting that a special issue on Complex Systems in Aesthetics and Arts is being published. As the editors of this special issue, we would like to thank the reviewers of the submitted papers for their hard work in making this issue possible, as well as the authors who submitted their work and were very responsive to the comments of the reviewers and editors.

The word complexity has a specific meaning in the context of “complex systems” research, as the study of systems made of many components—not in themselves necessarily complex—that through loosely coupled, local interactions generate complex, emergent behaviours. Such systems have the potential to act as the basis for the production of artworks, whether entirely computer generated or as a result of a cocreative system between humans and computers. Such art might make its impact through the intrinsic interest of the complex behaviour in the system, by representing, exploring, or connoting some worldly aspect of complexity, or by using complex systems as a way of exploring a space of possible works. Furthermore, complex systems research has the potential to simulate emergent processes in the artworld, such as the interaction between artists, audiences, and critics, or the development of aesthetic ideas or artistic fashions over time.

 

Complex Systems in Aesthetics and Arts
Juan Romero, Colin Johnson, and Jon McCormack

Complexity
Volume 2019, Article ID 9836102, 2 pages

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The stochastic thermodynamics of computation

(...) In this paper I review some of this recent work on the 'stochastic thermodynamics of computation'. After reviewing the salient parts of information theory, computer science theory, and stochastic thermodynamics, I summarize what has been learned about the entropic costs of performing a broad range of computations, extending from bit erasure to loop-free circuits to logically reversible circuits to information ratchets to Turing machines. These results reveal new, challenging engineering problems for how to design computers to have minimal thermodynamic costs. They also allow us to start to combine computer science theory and stochastic thermodynamics at a foundational level, thereby expanding both.

 

The stochastic thermodynamics of computation
David H Wolpert
Journal of Physics A: Mathematical and Theoretical, Volume 52, Number 19
Shannon's Information Theory 70 years on

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Towards a quantitative model of epidemics during conflicts 

Epidemics may both contribute to and arise as a result of conflict. The effects of conflict on infectious diseases are complex and there have been confounding observations of both increase and decrease in disease outbreaks during and after conflicts. However there is no unified mathematical model that explains all these counter-intuitive observations. There is an urgent need for a quantitative framework for modelling conflicts and epidemics. We introduce a set of mathematical models to understand the role of conflicts in epidemics. Our mathematical framework has the potential to explain the counterintuitive observations and the complex role of human conflicts in epidemics. Our work suggests that aid and peacekeeping organizations should take an integrated approach that combines public health measures, socio-economic development, and peacekeeping in the conflict zone. Our approach exemplifies the role of non-linear thinking in complex systems like human societies. We view our work as a step towards a quantitative model of disease spread in conflicts.

 

Banerjee S. 2019. Towards a quantitative model of epidemics during conflicts. PeerJ Preprints 7:e27651v1 https://doi.org/10.7287/peerj.preprints.27651v1

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Topical Alignment in Online Social Systems

Topical Alignment in Online Social Systems | Papers | Scoop.it

Understanding the dynamics of social interactions is crucial to comprehend human behavior. The emergence of online social media has enabled access to data regarding people relationships at a large scale. Twitter, specifically, is an information oriented network, with users sharing and consuming information. In this work, we study whether users tend to be in contact with people interested in similar topics, i.e., if they are topically aligned. To do so, we propose an approach based on the use of hashtags to extract information topics from Twitter messages and model users' interests. Our results show that, on average, users are connected with other users similar to them. Furthermore, we show that topical alignment provides interesting information that can eventually allow inferring users' connectivity. Our work, besides providing a way to assess the topical similarity of users, quantifies topical alignment among individuals, contributing to a better understanding of how complex social systems are structured.

 

Topical Alignment in Online Social Systems

Felipe Maciel Cardoso, Sandro Meloni, André Santanchè, and Yamir Moreno

Front. Phys., 17 April 2019 | https://doi.org/10.3389/fphy.2019.00058

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Mind, Body, Quantum Mechanics

I discuss the following: The causal closure of classical physics implies that consciousness in a classical physics brain can at best be epiphenomenal. Quantum mechanics can break the causal closure of classical physics in two ways: measurement and a newly discovered Poised Realm. Conscious experience may be associated with quantum measurement. Here quantum mind has acausal consequences for the classical brain. I propose genetic experiments to test this. Entanglement may solve the “binding problem.” I believe these proposals unite mind and body in a new way and answer Descartes after 350 years of the Stalemate introduced by his dualism of Res cogitans and Res extensa.

 

Mind, Body, Quantum Mechanics
Stuart Kauffman

Activitas Nervosa Superior

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‘Liquid brains, solid brains: How distributed cognitive architectures process information

‘Liquid brains, solid brains: How distributed cognitive architectures process information | Papers | Scoop.it

Theme issue ‘Liquid brains, solid brains: How distributed cognitive architectures process information’ compiled and edited by Ricard Solé, Melanie Moses and Stephanie Forrest

Philosophical Transactions of the Royal Society B: Biological Sciences

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Modeling Small Systems Through the Relative Entropy Lattice

There are certain contexts, where we would like to analyze the behavior of small interacting systems, such as sports teams. While large interacting systems have drawn much attention in the past years, let it be physical systems of interacting particles or social networks, small systems are short of appropriate quantitative modeling and measurement tools. We propose a simple procedure for analyzing a small system through the degree in which its behavior at different granularity levels (e.g., dyads) non-linearly diverges from the simple additive behavior of its sub-units. For example, we may model the behavior of a soccer team by measuring the extent to which the behavior changes when we move from individual players to dyads, triads, and so on. In this paper, we address the challenge of modeling small systems in terms of measuring divergence from additivity at different granularity levels of the system. We present and develop a measure for quantifying divergence from additivity through what we term a Relative Entropy Lattice , and illustrate its benefits in modeling the behavior of a specific small system, a soccer team, using data from the English Premier League. Our method has practical implications too, such as allowing the coach to identify “hidden” weak spots in the team’s behavior.

 

Modeling Small Systems Through the Relative Entropy Lattice
Yair Neuman ; Dan Vilenchik

IEEE Access ( Volume: 7 )
Page(s): 43591 - 43597

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