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Re-conceptualizing the origins of life

Complexity Digest - Sun, 11/19/2017 - 09:27

Over the last several hundred years of scientific progress, we have arrived at a deep understanding of the non-living world. We have not yet achieved an analogous, deep understanding of the living world. The origins of life is our best chance at discovering scientific laws governing life, because it marks the point of departure from the predictable physical and chemical world to the novel, history-dependent living world. This theme issue aims to explore ways to build a deeper understanding of the nature of biology, by modelling the origins of life on a sufficiently abstract level, starting from prebiotic conditions on Earth and possibly on other planets and bridging quantitative frameworks approaching universal aspects of life. The aim of the editors is to stimulate new directions for solving the origins of life. The present introduction represents the point of view of the editors on some of the most promising future directions.


Re-conceptualizing the origins of life
Sara I. Walker, N. Packard, G. D. Cody
Published 13 November 2017.DOI: 10.1098/rsta.2016.0337

Source: rsta.royalsocietypublishing.org

Building Codes for Bacterial Cities | Quanta Magazine

Complexity Digest - Sat, 11/18/2017 - 15:53

Biofilms are bacterial fortresses, but understanding how hydrodynamics and competition shape their architecture could reveal their subtle weaknesses.

Source: www.quantamagazine.org

The Beautiful Intelligence of Bacteria and Other Microbes

Complexity Digest - Fri, 11/17/2017 - 15:53

Bacterial biofilms and slime molds are more than crude patches of goo. Detailed time-lapse microscopy reveals how they sense and explore their surroundings,

Source: www.quantamagazine.org

6th Roundtable Teotihuacan

Dr. Tom Froese - Thu, 11/16/2017 - 13:58

Today started the 6th Roundtable of Teotihuacan, which will take place in Teotihuacan during Nov. 16-18, 2017.

There is live transmission of the main talks: http://www.inah.gob.mx/es/mesa-teotihuacan-programa

The title and abstract of my talk are as follows:

Explorando la función del posible cogobierno de distritos con base en un modelo matemático de su red social

Dr. Tom Froese y Dra. Linda R. Manzanilla

Los expertos siguen divididos sobre la naturaleza del sistema sociopolítico de la antigua ciudad de Teotihuacan. A pesar del poco éxito, la excavaciones en el área continúan con la esperanza de encontrar pruebas convincentes de poderosas dinastías de gobernantes, como una tumba real. Sin embargo, la posibilidad alterna de un gobierno colectivo también requiere de más evidencia y además de que sigue siendo poco entendida en términos teóricos. Por un lado hay una ausencia de evidencia de una burocratización de alto nivel. Por otro lado parece que una red descentralizada, y compuesta sólo de múltiples gobernantes de barrio, es susceptible a los problemas de asegurar la cooperación bajo de condiciones de acción colectiva. Dada la actual pobreza de evidencia directa sobre la forma de gobierno de la ciudad, y la falta de claridad teórica acerca de qué formas de gobierno podrían haber sido factibles, otra posibilidad para avanzar es explorar de forma más sistemática el espacio de hipótesis viables. En un trabajo previo utilizamos un modelo matemático para mostrar que en principio la preocupación sobre si una estrategia colectiva podría funcionar es infundada, siempre y cuando supongamos que la topología de su red social pudiera ser transformada a través de rituales comunitarios y no estuviera fuertemente subdividida en distritos. Hemos ampliado este modelo para comprobar si el aumento de la jerarquía social, a través de la inclusión de cuatro cogobernantes al nivel de cuatro distritos, podría superar el impedimento a la cooperación que surge de fuertes divisiones entre dichos distritos. Encontramos una sinergia especial entre la influencia jerárquica y el ritual comunitario en que sólo su combinación mejoró el grado de la coordinación entre los gobernantes de todos niveles. Este resultado es consistente con las representaciones artísticas de la élite Teotihuacana que enfatizan su papel de ser especialistas en rituales que sirven al bien público, en lugar de ser lideres con poder político centralizado actuando en contextos seculares.


A Plea for not Watering Down the Unseemly: Reconsidering Francisco Varela’s Contribution to Science

Complexity Digest - Wed, 11/15/2017 - 18:10

Context: In the past three decades, the work of Varela has had an enormous impact on current developments in contemporary science. Problem: Varela’s thought was extremely complex and multifaceted, and while some aspects – notably his contributions to the autopoietic theory of living and enactivist approach to cognition – have gained widespread acclaim, others have been ignored or watered down. Method: We identify three dimensions of Varela’s thought: (i) anti-realism of the “middle way”; (ii) anti-foundationalism of the circular/recursive onto-epistemology; and (iii) ethical/social implications of the circularity/recursivity. The discussion of these dimensions is followed by a concise overview of the individual target articles in this issue and the topics they cover. Finally, we discuss in what ways the articles extend and relate to Varela’s work. We do this by means of a concrete example: the relation between “enaction” and “enactivism. Results: We show that the ignoring-cum-watering-down process of Varela’s contributions to science is at least partly linked to the three dimensions of Varela’s thought. Based on our examination we also find that the more narrow research topics are always interrelated with broader philosophical reflection. Researching into ignored and watered-down aspects of Varela’s work enables us to not only gain fresh insights into Varela’s overall philosophy and rekindle interest in the topics and themes that have been brushed aside, but also cast a fresh light on those that are currently in full bloom. Implications: Reviving interest in Varela’s work in toto could lead to fruitful research and discussion in numerous scientific fields. To illustrate this idea, we delineate, tentatively, three domains – theoretical, empirical, and existential – where Varela’s contribution to philosophy and science could instigate prolific exchange of views. Constructivist content: All three dimensions of Varela’s philosophy have strong affinities with radical constructivist critique of realism and some of its epistemological and ethical implications.


A Plea for not Watering Down the Unseemly: Reconsidering Francisco Varela’s Contribution to Science
Sebastjan Vörös & Alexander Riegler

Source: www.univie.ac.at

Mathematical Work of Francisco Varela

Complexity Digest - Wed, 11/15/2017 - 16:10

Purpose: This target article explicates mathematical themes in the work of Varela that remain of current interest in present-day second-order cybernetics. Problem: Varela’s approach extended biological autonomy to mathematical models of autonomy using reflexivity, category theory and eigenform. I will show specific ways that this mathematical modeling can contribute further to both biology and cybernetics. Method: The method of this article is to use elementary mathematics based in distinctions (and some excursions into category theory and other constructions that are also based in distinctions) to consistently make all constructions and thereby show how the observer is involved in the models that are so produced. Results: By following the line of mathematics constructed through the imagination of distinctions, we find direct access and construction for the autonomy postulated by Varela in his book Principles of Biological Autonomy. We do not need to impose autonomy at the base of the structure, but rather can construct it in the context of a reflexive domain. This sheds new light on the original approach to autonomy by Varela, who also constructed autonomous states but took them as axiomatic in his calculus for self-reference. Implications: The subject of the relationship of mathematical models, eigenforms and reflexivity should be reexamined in relation to biology, biology of cognition and cybernetics. The approach of Maturana to use only linguistic and philosophical approaches should now be reexamined and combined with Varela’s more mathematical approach and its present-day extensions.


Mathematical Work of Francisco Varela
Louis H. Kauffman

Source: www.univie.ac.at

Enacting Enaction: A Dialectic Between Knowing and Being

Complexity Digest - Wed, 11/15/2017 - 14:09

Context: The notion of “enaction,” as originally expounded by Varela and his colleagues, was introduced into cognitive science as part of a broad philosophical framework combining science, phenomenology, and Buddhist philosophy. Its intention was to help the researchers in the field avoid falling prey to various dichotomies (mind/body, self/world, self/other) bedeviling modern philosophy and science, and serve as a “conceptual evocation” of “non-duality” or “groundlessness: an ongoing and irreducible circulation between the flux of lived experience (being) and the search of reason for conceptual invariants (knowing. Problem: It seems that, within the burgeoning field of “enactivism,” these far-reaching dimensions of the original proposal are often either dismissed or simply ignored. For this reason, the article tries to answer the following questions: Does the move away from the original exposition of enaction matter? What, if anything, has been lost along the way? What are the implications of the elements that have been discarded? Method: By drawing on some of the less well-known works of Varela, we spell out and elucidate some of the more radical aspects of the notion of enaction and the broader philosophical framework into which it was originally embedded. Results: We argue that this broader philosophical framework is of utmost importance, as it shows that enaction is only one part of the multi-layered “change in the context” that Varela felt was needed to successfully instantiate a move towards the non-dual. This “change of context” involves not only a change in the way we think about dualities, but also a change in the way we experience them. The role of new scientific metaphors, such as enaction (but also autopoiesis, embodiment, etc.), is to function as conceptual evocations of this back-and-forth exchange between knowing and being. However, if this overall framework is discarded, as is often the case in contemporary accounts, enaction loses its radical impetus and becomes mellowed down to yet another version of naturalized epistemology. Implications: Taking the notion of enaction seriously implies a radical shift in our conceptions of science and knowledge, as it encompasses a theoretical and existential move away from a detached observer to embedded and engaged cognizer. Thus, our manner of thinking can no longer be considered in isolation from our manner of being, which indicates a deep interconnection between epistemology and ethics, and may entail profound changes in the definition of the aims, methods, and values of the research community: self-transformation as a consequence of, and condition for, understanding. Constructivist content: The target article advocates a critical approach to realist presuppositions in contemporary science and philosophy, and emphasizes a deep interrelation between being and knowing, between ethics and epistemology.


Enacting Enaction: A Dialectic Between Knowing and Being
Sebastjan Vörös & Michel Bitbol

Source: www.univie.ac.at

XLVII Winter Meeting on Statistical Physics 2018

Complexity Digest - Tue, 11/14/2017 - 23:32

The purpose of the meeting is to bring together the national community of physicists working on statistical physics and related areas, in order to exchange knowledge, results and discuss new lines of research.  We also invite a group of internationally-well known scientists who have made fundamental contributions in their respective fields. This provides the opportunity to exchange ideas between national and foreign colleagues in a pleasant, inclusive and informal environment.
The main program consists of plenary lectures given by selected invited speakers who present, in a non-technical way the “state of the art” in their fields of study, as well as their main contributions to the field. We invite students and postdocs to submit abstracts by December 5th to be considered in the poster session.


The XLVII Winter Meeting on Statistical Physics will take place in the city of Puebla, Puebla, México

from the 07th to the 10th of January 2018

Source: sites.google.com

Is there room for normativity in a dynamical world?

Dr. Tom Froese - Tue, 11/14/2017 - 13:36

Tomorrow at 2pm I will be giving an online talk for the ENactive Seminars Online (ENSO) Series. Here are the title and abstract:

Is there room for normativity in a dynamical world?

Enactivism rejects the standard working hypothesis of cognitive science, according to which all cognition involves the unconscious manipulation of mental representations, and replaces it with a dynamical systems account. And yet enactivism resists other, purely dynamical approaches that see no role for any kind of subjectivity, because it appeals to the role of our lived phenomenology and claims that living beings behave with respect to norms directed at maintaining their viability.

So far, this middle way seems to be philosophically unsatisfactory: at best it allows us to claim that acting in accordance with experience or norms just is a certain kind of dynamic pattern. But this turns subjectivity into a mysterious difference that makes no difference as such with respect to the unfolding of those patterns, which is completely determined by the dynamics alone.

This calls for deeper philosophical reflection about how it is possible for subjectivity to play a role in an objective world while avoiding a regression to the untenable positions of either representationalism or eliminativism.

Watch the seminar live: http://www.ensoseminars.com/presentations/past17/

Social Systems Programming I: neural and behavioral control mechanisms

Complexity Digest - Tue, 11/14/2017 - 09:00

Social systems can be defined as autopoietic networks of distinctions and rules that specify which actions should be performed under which conditions. Social systems have an enormous power over human individuals, as they can “program” them to sacrifice resources, happiness, loved ones and even themselves to the perpetuation of the system—as exemplified by religious celibacy, honor killings and suicide bombings. Such overriding of the biological instincts of survival and procreation demands powerful control mechanisms. The present paper surveys some of the basic neural and behavioral mechanisms used for programming within social systems, and is followed by another paper surveying emotional and structural mechanism. Basic conditioning happens through rewarding or reinforcement of socially sanctioned actions. Its power is extended by the conformist transmission of narratives that promise as yet virtual rewards, and by ritualized behaviors that suppress non-conforming beliefs through cognitive dissonance. Through such mechanisms, social systems commonly impede individual emancipation, self-actualization and societal progress.


Social Systems Programming I: neural and behavioral control mechanisms Francis Heylighen, Marta Lenartowicz, Kate Kingsbury, Shima Beigi & Tjorven Harmsen  

Source: www.academia.edu

It should be noted that similar mechanisms are also useful for promoting cooperation and limiting selfish behaviors.

Constraints on physical reality arising from a formalization of knowledge

Complexity Digest - Mon, 11/13/2017 - 10:38

There are (at least) four ways that an agent can acquire information concerning the state of the universe: via observation, control, prediction, or via retrodiction, i.e., memory. Each of these four ways of acquiring information seems to rely on a different kind of physical device (resp., an observation device, a control device, etc.). However it turns out that certain mathematical structure is common to those four types of device. Any device that possesses a certain subset of that structure is known as an “inference device” (ID).
Here I review some of the properties of IDs, including their relation with Turing machines, and (more loosely) quantum mechanics. I also review the bounds of the joint abilities of any set of IDs to know facts about the physical universe that contains them. These bounds constrain the possible properties of any universe that contains agents who can acquire information concerning that universe.
I then extend this previous work on IDs, by adding to the definition of IDs some of the other mathematical structure that is common to the four ways of acquiring information about the universe but is not captured in the (minimal) definition of IDs. I discuss these extensions of IDs in the context of epistemic logic (especially possible worlds formalisms like Kripke structures and Aumann structures). In particular, I show that these extensions of IDs are not subject to the problem of logical omniscience that plagues many previously studied forms of epistemic logic.


Constraints on physical reality arising from a formalization of knowledge
David Wolpert

Source: arxiv.org

Dissipative structures and irreversibility in nature: Celebrating 100th birth anniversary of Ilya Prigogine (1917–2003)

Complexity Digest - Sun, 11/12/2017 - 09:39

Friends and colleagues who knew Ilya Prigogine well called him “A poet of thermodynamics.” It is an apt description. When Prigogine talked about thermodynamics and irreversible processes, one had the sense he understood or knew more than what his words conveyed. Natural processes all around us are irreversible; it is a fact. Their consequence is not merely to increase the entropy of the universe and destroy order. They can also do the opposite: create highly ordered complex structures with extraordinary properties and create life itself. Prigogine saw this as a profound aspect of nature that thermodynamics has revealed. When he came across the famed South Indian sculpture of Nataraja, the dancing Shiva, that depicts as a cosmic dance the perfect balance between creation and destruction that originate from the same source, he made sure he had a bronze statue of Nataraja of highest artistic quality in his art collection. A picture of it became the cover art for the book Thermodynamic Theory of Structure Stability and Fluctuations, that he coauthored with Paul Glansdorff. It was poetry of thermodynamics, creation and destruction emerging from a common source, a perfectly balanced cosmic dance. One could surmise all this from Prigogine’s discourses on thermodynamics.


Dissipative structures and irreversibility in nature: Celebrating 100th birth anniversary of Ilya Prigogine (1917–2003)
Chaos 27, 104501 (2017); https://doi.org/10.1063/1.5008858
Dilip Kondepudi, Tomio Petrosky, and John A. Pojman

Source: aip.scitation.org

The Unforgiving Math That Stops Epidemics

Complexity Digest - Sat, 11/11/2017 - 13:21

As the annual flu season approaches, medical professionals are again encouraging people to get flu shots. Perhaps you are among those who rationalize skipping the shot on the grounds that “I never get the flu” or “if I get sick, I get sick” or “I’m healthy, so I’ll get over it.” What you might not realize is that these vaccination campaigns for flu and other diseases are about much more than your health. They’re about achieving a collective resistance to disease that goes beyond individual well-being — and that is governed by mathematical principles unforgiving of unwise individual choices.

Source: www.quantamagazine.org

Characterizing the structural diversity of complex networks across domains

Complexity Digest - Sat, 11/11/2017 - 11:26

The structure of complex networks has been of interest in many scientific and engineering disciplines over the decades. A number of studies in the field have been focused on finding the common properties among different kinds of networks such as heavy-tail degree distribution, small-worldness and modular structure and they have tried to establish a theory of structural universality in complex networks. However, there is no comprehensive study of network structure across a diverse set of domains in order to explain the structural diversity we observe in the real-world networks. In this paper, we study 986 real-world networks of diverse domains ranging from ecological food webs to online social networks along with 575 networks generated from four popular network models. Our study utilizes a number of machine learning techniques such as random forest and confusion matrix in order to show the relationships among network domains in terms of network structure. Our results indicate that there are some partitions of network categories in which networks are hard to distinguish based purely on network structure. We have found that these partitions of network categories tend to have similar underlying functions, constraints and/or generative mechanisms of networks even though networks in the same partition have different origins, e.g., biological processes, results of engineering by human being, etc. This suggests that the origin of a network, whether it’s biological, technological or social, may not necessarily be a decisive factor of the formation of similar network structure. Our findings shed light on the possible direction along which we could uncover the hidden principles for the structural diversity of complex networks.


Characterizing the structural diversity of complex networks across domains
Kansuke Ikehara, Aaron Clauset

Source: arxiv.org

Phase Coexistence in Insect Swarms

Complexity Digest - Fri, 11/10/2017 - 15:47

Animal aggregations are visually striking, and as such are popular examples of collective behavior in the natural world. Quantitatively demonstrating the collective nature of such groups, however, remains surprisingly difficult. Inspired by thermodynamics, we applied topological data analysis to laboratory insect swarms and found evidence for emergent, material-like states. We show that the swarms consist of a core “condensed” phase surrounded by a dilute “vapor” phase. These two phases coexist in equilibrium, and maintain their distinct macroscopic properties even though individual insects pass freely between them. We further define a pressure and chemical potential to describe these phases, extending theories of active matter to aggregations of macroscopic animals and laying the groundwork for a thermodynamic description of collective animal groups.


Phase Coexistence in Insect Swarms
Michael Sinhuber and Nicholas T. Ouellette
Phys. Rev. Lett. 119, 178003 – Published 24 October 2017

Source: journals.aps.org

Large-scale study of social network structure and team performance in a multiplayer online game

Complexity Digest - Fri, 11/10/2017 - 13:46

A question of interest in both theory and practice is if and how familiarity between members of a team, expressed in terms of social network structure, relates to the success of the team in a given task. In this paper we revisit this important question in a novel manner by employing game outcome statistics from Dota 2, a popular team-based multiplayer online game, combined with network data from Steam Community, a social networking service for gamers. We conduct a large-scale analysis of 4168 teams to study how network density, and the minimum and maximum degree of the within-team social network are associated with team performance, and determine how this association is moderated by team skill. We observe that minimum degree is strongly associated with good performance, especially in teams with lower skill. Together with previous results on network density that we corroborate in this paper, our findings suggest that a successful team is not only moderately connected overall, but its members should also individually have not too few nor too many within team connections.


Large-scale study of social network structure and team performance in a multiplayer online game
Antti Ukkonen, Juho Hamari

Source: arxiv.org

Measuring Influence in Science: Standing on the Shoulders of Which Giants?

Complexity Digest - Fri, 11/10/2017 - 13:20

I study the measurement of the influence of scientists based on bibliographic data. I propose a new measure that accounts for indirect influence and allows to compare scientists across different fields of science. By contrast, common measures of influence that “count citations”, such as the h-index, are unable to satisfy either of these two properties. I use the axiomatic method in two opposite ways: to highlight the two limitations of citation-counting schemes and their independence, and to carefully justify the assumptions made in the construction of the proposed measure.


Measuring Influence in Science: Standing on the Shoulders of Which Giants?
Antonin Macé

Source: arxiv.org

Breaking the spell of nestedness

Complexity Digest - Fri, 11/10/2017 - 09:42

Mutualistic interactions, which are beneficial for both interacting species, are recurrently present in ecosystems. Observations of natural systems showed that, if we draw mutualistic relationships as binary links between species, the resulting bipartite network of interactions displays a widespread particular ordering called nestedness. On the other hand, theoretical works have shown that a nested structure has a positive impact on a number of relevant features ranging from species coexistence to a higher structural stability of communities and biodiversity. However, how nestedness emerges and what are its determinants, are still open challenges that have led to multiple debates to date. Here, we show, by applying a theoretical approach to the analysis of 167 real mutualistic networks, that nestedness is not an irreducible feature, but a consequence of the degree sequences of both guilds of the mutualistic network. Remarkably, we find that an outstanding majority of the analyzed networks does not show statistical significant nestedness. These findings point to the need of revising previous claims about the role of nestedness and might contribute to expanding our understanding of how evolution shapes mutualistic interactions and communities by placing the focus on the local properties rather than on global quantities.


Breaking the spell of nestedness
Claudia Payrato Borras, Laura Hernandez, Yamir Moreno
doi: https://doi.org/10.1101/216564

Source: www.biorxiv.org

Collective origins of the genetic code

Dr. Tom Froese - Thu, 11/09/2017 - 09:47

Later today I am giving the weekly colloquium at the Center for Complexity Sciences (C3) at our main campus of UNAM. The topic will be our ongoing work on a simulation model of the collective origins of the genetic code. Details of the colloquium below:

Self-referential basis of undecidable dynamics: from The Liar Paradox and The Halting Problem to The Edge of Chaos

Complexity Digest - Thu, 11/09/2017 - 05:17

In this paper we explore several fundamental relations between formal systems, algorithms, and dynamical systems, focussing on the roles of undecidability, universality, diagonalization, and self-reference in each of these computational frameworks. Some of these interconnections are well-known, while some are clarified in this study as a result of a fine-grained comparison between recursive formal systems, Turing machines, and Cellular Automata (CAs). In particular, we elaborate on the diagonalization argument applied to distributed computation carried out by CAs, illustrating the key elements of G\”odel’s proof for CAs. The comparative analysis emphasizes three factors which underlie the capacity to generate undecidable dynamics within the examined computational frameworks: (i) the program-data duality; (ii) the potential to access an infinite computational medium; and (iii) the ability to implement negation. The considered adaptations of G\”odel’s proof distinguish between computational universality and undecidability, and show how the diagonalization argument exploits, on several levels, the self-referential basis of undecidability.


Self-referential basis of undecidable dynamics: from The Liar Paradox and The Halting Problem to The Edge of Chaos
Mikhail Prokopenko, Michael Harré, Joseph Lizier, Fabio Boschetti, Pavlos Peppas, Stuart Kauffman

Source: arxiv.org


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