Complexity and Biology
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Network-Oriented Modeling - Jan Treur

Network-Oriented Modeling - Jan Treur | Complexity and Biology | Scoop.it

This book presents a new approach that can be applied to complex, integrated individual and social human processes. It provides an alternative means of addressing complexity, better suited for its purpose than and effectively complementing traditional strategies involving isolation and separation assumptions.
Network-oriented modeling allows high-level cognitive, affective and social models in the form of (cyclic) graphs to be constructed, which can be automatically transformed into executable simulation models. The modeling format used makes it easy to take into account theories and findings about complex cognitive and social processes, which often involve dynamics based on interrelating cycles. Accordingly, it makes it possible to address complex phenomena such as the integration of emotions within cognitive processes of all kinds, of internal simulations of the mental processes of others, and of social phenomena such as shared understandings and collective actions. A variety of sample models – including those for ownership of actions, fear and dreaming, the integration of emotions in joint decision-making based on empathic understanding, and evolving social networks – illustrate the potential of the approach. Dedicated software is available to support building models in a conceptual or graphical manner, transforming them into an executable format and performing simulation experiments. The majority of the material presented has been used and positively evaluated by undergraduate and graduate students and researchers in the cognitive, social and AI domains.
Given its detailed coverage, the book is ideally suited as an introduction for graduate and undergraduate students in many different multidisciplinary fields involving cognitive, affective, social, biological, and neuroscience domains.

 

Network-Oriented Modeling
Addressing Complexity of Cognitive, Affective and Social Interactions
Jan Treur


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[1607.00462] Suppression of chaos through coupling to an external chaotic system

[1607.00462] Suppression of chaos through coupling to an external chaotic system | Complexity and Biology | Scoop.it
We explore the behaviour of an ensemble of chaotic oscillators coupled only to an external chaotic system, whose intrinsic dynamics may be similar or dissimilar to the group. Counter-intuitively, we find that a dissimilar external system manages to suppress the intrinsic chaos of the oscillators to fixed point dynamics, at sufficiently high coupling strengths. So, while synchronization is induced readily by coupling to an identical external system, control to fixed states is achieved only if the external system is dissimilar. We quantify the efficacy of control by estimating the fraction of random initial states that go to fixed points, a measure analogous to basin stability. Lastly, we indicate the generality of this phenomenon by demonstrating suppression of chaotic oscillations by coupling to a common hyper-chaotic system. These results then indicate the easy controllability of chaotic oscillators by an external chaotic system, thereby suggesting a potent method that may help design control strategies.

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Brian Castellani on the Complexity Sciences

Brian Castellani on the Complexity Sciences | Complexity and Biology | Scoop.it
Brian Castellani on the Fast Growing Complexity Sciences and their Controversial Tangle with Social Inquiry   In this commentary piece for the TCS website, Brian Castellani reflects on the fast gro...
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aSSB'16 - Call for Student Workshop Papers

aSSB'16 - Call for Student Workshop Papers | Complexity and Biology | Scoop.it
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Costas Bouyioukos's curator insight, November 6, 2015 9:21 AM
Dear Colleague,


The Thematic School “advances in Systems and Synthetic Biology - Modelling Complex Biological Systems in the Context of Genomics” aSSB'16 will be held in Evry on March 21-25, 2016 ( http://epigenomique.free.fr/en/index.php ;).


We are organising an international workshop for students (PhD and M2) and post-doctoral fellows. This workshop offers the opportunity for students and post-doctoral fellows to get an official recognition through peer-review, to discuss their projects and to get feedback from other participants by sharing their experience in a favorable environment.  The M2, PhD or post-doc projects can concern either an introductory presentation, works in progress or some first conclusive results. Topics of interest include any contribution helping to understand or to engineer biological systems by using models coming from biology, physics, chemistry, engineering, computer sciences or mathematics.


Submission procedure: The short paper (between 3 and 8 pages in A4 format) should be written in English, with at least a M2, PhD student or post-doctoral fellow among the authors. It will be reviewed by the scientific committee of the School. Once the paper is accepted, the student must attend the workshop and present their work in English during a 15 minutes-presentation. They are also encouraged to bring a poster. Free registration is proposed to one of the authors (M2, PhD, post-doc) of an accepted paper. The accepted papers will be published in the proceedings book of the School.

Details and instructions for the submissions can be found at: http://epigenomique.free.fr/en/exp_etudiant.php

Important dates for the submission of articles:
- Submission of short papers: before December 14, 2015
- Notification of acceptance / revision / rejection: January 11, 2016
- Deadline for submission of revised manuscripts: January 25, 2016

Best wishes,
The aSSB'16 scientific board
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Doctoral Program in Complexity Sciences

Doctoral Program in Complexity Sciences | Complexity and Biology | Scoop.it

The Doctoral Program in Complexity Sciences provides an integrated training that enable doctoral students understand the environment in which they live, by applying modelling methods and computer simulation, and solve complex problems using information technology, including support systems to organizational processes in complex environments. Developing these skills will enable the integration of multidisciplinary knowledge and the autonomously formulation of judgements from data that is often incomplete.


The Doctoral Program in Complexity Sciences is taught in ISCTE and FCUL. It has an international dimension based on a set of protocols to the Paris-Dauphine University (France), with the University of Savoie (France) and the Academy of Economic Studies of Bucharest (Romania). There are teachers of exchanges with the University Paul Sabatier in Toulouse (France), with the Open University (UK), with the University of Utrecht (Netherlands) and the University of Texas (USA).

 

The new curriculum comprehends a 1st curricular year and a 2nd and 3rd years mainly dedicated to research at PhD level. Students are invited to develop their research projects at LabMAg (FCUL, Lisbon), ISTAR (ISCTE-IUL, Lisbon), and IITGn (Gandhinagar, India).

 

A new class for the 1st curricular year will start in February 2016. Classes will take place on Tuesdays and Wednesdays, from 18h to 21h30.

 

Applications for the 1st curricular year are open until the 23rd of December, 2015. Applications are submitted through the form available at the ISCTE-IUL applications website.


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Interdisciplinarity

Interdisciplinarity | Complexity and Biology | Scoop.it

Nature’s special issue probes how scientists and social scientists are coming together to solve the grand challenges of energy, food, water, climate and health. This special scrutinizes the data on interdisciplinary work and looks at its history, meaning and funding. A case study and a reappraisal of the Victorian explorer Richard Francis Burton explore the rewards of breaking down boundaries. Meanwhile, a sustainability institute shares its principles for researchers who work across disciplines. Thus inspired, we invite readers to test their polymathy in our lighthearted quiz.


http://www.nature.com/news/interdisciplinarity-1.18295 ;


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Topological effects of network structure on long-term social network dynamics in a wild mammal

Social structure influences ecological processes such as dispersal and invasion, and affects survival and reproductive success. Recent studies have used static snapshots of social networks, thus neglecting their temporal dynamics, and focused primarily on a limited number of variables that might be affecting social structure. Here, instead we modelled effects of multiple predictors of social network dynamics in the spotted hyena, using observational data collected during 20 years of continuous field research in Kenya. We tested the hypothesis that the current state of the social network affects its long-term dynamics. We employed stochastic agent-based models that allowed us to estimate the contribution of multiple factors to network changes. After controlling for environmental and individual effects, we found that network density and individual centrality affected network dynamics, but that social bond transitivity consistently had the strongest effects. Our results emphasise the significance of structural properties of networks in shaping social dynamics.

 

Topological effects of network structure on long-term social network dynamics in a wild mammal
Amiyaal Ilany, Andrew S. Booms and Kay E. Holekamp

Ecology Letters
Early View

http://dx.doi.org/10.1111/ele.12447


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Ingenious: David Krakauer

Ingenious: David Krakauer | Complexity and Biology | Scoop.it

So one way of thinking about complexity is adaptive, many body systems. The sun is not an adaptive system; the sun doesn’t really learn. These do; these are learning systems. And we’ve never really successfully had a theory for many body learning systems. So just to make that a little clearer, the brain would be an example. There are many neurons interacting adaptively to form a representation, for example, of a visual scene; in economy, there are many individual agents deciding on the price of a good, and so forth; a political system voting for the next president. All of these systems have individual entities that are heterogeneous and acquire information according to a unique history about the world in which they live. That is not a world that Newton could deal with. There’s a very famous quote where he says something like, I have been able to understand the motion of the planets, but I will never understand the madness of men. What Newton was saying is, I don’t understand complexity.

 

http://nautil.us/issue/23/dominoes/ingenious-david-krakauer


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To Explain the World: The Discovery of Modern Science (by Steven Weinberg)

To Explain the World: The Discovery of Modern Science

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A masterful commentary on the history of science from the Greeks to modern times, by Nobel Prize-winning physicist Steven Weinberg—a thought-provoking and important book by one of the most distinguished scientists and intellectuals of our time.

In this rich, irreverent, and compelling history, Nobel Prize-winning physicist Steven Weinberg takes us across centuries from ancient Miletus to medieval Baghdad and Oxford, from Plato’s Academy and the Museum of Alexandria to the cathedral school of Chartres and the Royal Society of London. He shows that the scientists of ancient and medieval times not only did not understand what we understand about the world—they did not understand what there is to understand, or how to understand it. Yet over the centuries, through the struggle to solve such mysteries as the curious backward movement of the planets and the rise and fall of the tides, the modern discipline of science eventually emerged. Along the way, Weinberg examines historic clashes and collaborations between science and the competing spheres of religion, technology, poetry, mathematics, and philosophy.

 

 


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The Strange Inevitability of Evolution

The Strange Inevitability of Evolution | Complexity and Biology | Scoop.it

Natural selection supplies an incredibly powerful way of pruning variation into effective solutions to the challenges of the environment. But it can’t explain where all that variation came from. As the biologist Hugo de Vries wrote in 1905, “natural selection may explain the survival of the fittest, but it cannot explain the arrival of the fittest.” Over the past several years, Wagner and a handful of others have been starting to understand the origins of evolutionary innovation. Thanks to their findings so far, we can now see not only how Darwinian evolution works but why it works: what makes it possible.

(...)

These ideas suggest that evolvability and openness to innovation are features not just of life but of information itself. That is a view long championed by Schuster’s sometime collaborator, Nobel laureate chemist Manfred Eigen, who insists that Darwinian evolution is not merely the organizing principle of biology but a “law of physics,” an inevitable result of how information is organized in complex systems. And if that’s right, it would seem that the appearance of life was not a fantastic fluke but almost a mathematical inevitability.

 


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Reaction-Diffusion Processes on Interconnected Scale-Free Networks

We study the two particle annihilation reaction A+B->Ø A+B→∅ on interconnected scale free networks. We show that the mixing of particles and the evolution of the process are influenced by the number of interconnecting links and by their functional properties, while surprisingly when the interconnecting links have the same function as the links within the networks, they are not affected by the interconnectivity strategies in use. Due to the better mixing, which suppresses the segregation effect, we show that the reaction rates are faster than what was observed in other topologies, in-line with previous studies performed on single scale free networks.


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Inheritance: How Our Genes Change Our Lives - and Our Lives Change Our Genes (by Sharon Moalem MD PhD)

Inheritance: How Our Genes Change Our Lives--and Our Lives Change Our Genes

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Conventional wisdom dictates that our genetic destiny is fixed at conception. But Dr. Moalem's groundbreaking book shows us that the human genome is far more fluid. By bringing us to the bedside of his unique and complex patients, he masterfully demonstrates what rare genetic conditions can teach us all about our own health and well-being. Drawing on bleeding-edge science and sometimes heartbreaking stories of individuals he’s treated for rare genetic anomalies, Moalem explains how your DNA’s constant shape-shifting is “mediated and orchestrated by how you live, where you live, the stresses you face, and the things you consume.”


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The end of Moore's law: Living without an exponential increase in the efficiency of computational facilities

Since more than 50 years scientific and nonscientific communities are accustomed to computational facilities, which increase steadily in speed and efficiency of calculations, in particular in processor performance, memory size, and storage capacity. Mitchell Waldrop analyzes the current situation in the chip producing industry and predicts the end of Moore's prophecy of an exponential growth in computational capacities [1]. Here, an attempt is made to view with the eyes of a user the spectacular development of computers, its benefits for mathematics, science, and engineering as well as the possible consequences of its end.

 

The end of Moore's law: Living without an exponential increase in the efficiency of computational facilities
Peter Schuster

Complexity


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How Big Data Is Turning the World Into a Global Prison - and How to Change This

Talk took place at Lipari Summer School - Italy, June 2016 (see http://lipari.cs.unict.it/LipariSchool/ComplexSocialSystems/ )

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Jean-Michel Coron - "La régulation des systèmes complexes depuis Maxwell"

BnF - 11 mai 2011 Conférence donnée dans le cadre du cycle "Un texte, un mathématicien", organisée par la Société…

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Mechanisms of mutational robustness in transcriptional regulation

Robustness is the invariance of a phenotype in the face of environmental or genetic change. The phenotypes produced by transcriptional regulatory circuits are gene expression patterns that are to some extent robust to mutations. Here we review several causes of this robustness. They include robustness of individual transcription factor binding sites, homotypic clusters of such sites, redundant enhancers, transcription factors, redundant transcription factors, and the wiring of transcriptional regulatory circuits. Such robustness can either be an adaptation by itself, a byproduct of other adaptations, or the result of biophysical principles and non-adaptive forces of genome evolution. The potential consequences of such robustness include complex regulatory network topologies that arise through neutral evolution, as well as cryptic variation, i.e., genotypic divergence without phenotypic divergence. On the longest evolutionary timescales, the robustness of transcriptional regulation has helped shape life as we know it, by facilitating evolutionary innovations that helped organisms such as flowering plants and vertebrates diversify.

 

Mechanisms of mutational robustness in transcriptional regulation
Joshua L. Payne and Andreas Wagner

Front. Genet., 27 October 2015 | http://dx.doi.org/10.3389/fgene.2015.00322


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How scientists fool themselves – and how they can stop : Nature News & Comment

How scientists fool themselves – and how they can stop : Nature News & Comment | Complexity and Biology | Scoop.it
Humans are remarkably good at self-deception.
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Distributed Genius: Advancing the Growth of Linux - YouTube

Since its inception 20 years ago, the Linux operating system has become the most widely used software in the world. This is due to the thousands of minds fro...
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Probably the best promotion video that has ever been done for Linux!
Brilliant!
Great job by the "Linux Foundation"!

... even though some people (rightfully) say that it should be called GNU/Linux! 

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Complex Adaptive Systems: 10 Self-Organization Far-From-Equelibrium - YouTube

In this module we will be talking about the theory of far-from-equilibrium self-organization, we will firstly discuss the concepts of order and randomness in...

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Christophe Bredillet's curator insight, June 10, 2015 1:03 PM

A worthwhile series of video on Complex Adaptive Systems

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Quantum Adaptivity in Biology: From Genetics to Cognition (by Masanari Asano et al.)

Quantum Adaptivity in Biology: From Genetics to Cognition

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This book examines information processing performed by bio-systems at all scales: from genomes, cells and proteins to cognitive and even social systems. It introduces a theoretical/conceptual principle based on quantum information and non-Kolmogorov probability theory to explain information processing phenomena in biology as a whole.

The book begins with an introduction followed by two chapters devoted to fundamentals, one covering classical and quantum probability, which also contains a brief introduction to quantum formalism, and another on an information approach to molecular biology, genetics and epigenetics. It then goes on to examine adaptive dynamics, including applications to biology, and non-Kolmogorov probability theory.

Next, the book discusses the possibility to apply the quantum formalism to model biological evolution, especially at the cellular level: genetic and epigenetic evolutions. It also presents a model of the epigenetic cellular evolution based on the mathematical formalism of open quantum systems. The last two chapters of the book explore foundational problems of quantum mechanics and demonstrate the power of usage of positive operator valued measures (POVMs) in biological science.

 

 


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Complexity and the Arrow of Time: Charles H. Lineweaver, Paul C. W. Davies, Michael Ruse: 9781107027251: Amazon.com: Books

Complexity and the Arrow of Time

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Complexity and the Arrow of Time [Charles H. Lineweaver, Paul C. W. Davies, Michael Ruse] on Amazon.com. *FREE* shipping on qualifying offers. There is a widespread assumption that the universe in general, and life in particular, is 'getting more complex with time'. This book brings together a wide range of experts in science

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Self-Organization, Emergence, and Constraint in Complex Natural Systems

Contemporary complexity theory has been instrumental in providing novel rigorous definitions for some classic philosophical concepts, including emergence. In an attempt to provide an account of emergence that is consistent with complexity and dynamical systems theory, several authors have turned to the notion of constraints on state transitions. Drawing on complexity theory directly, this paper builds on those accounts, further developing the constraint-based interpretation of emergence and arguing that such accounts recover many of the features of more traditional accounts. We show that the constraint-based account of emergence also leads naturally into a meaningful definition of self-organization, another concept that has received increasing attention recently. Along the way, we distinguish between order and organization, two concepts which are frequently conflated. Finally, we consider possibilities for future research in the philosophy of complex systems, as well as applications of the distinctions made in this paper.

 

Self-Organization, Emergence, and Constraint in Complex Natural Systems
Jonathan Lawhead

http://arxiv.org/abs/1502.01476


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Eli Levine's curator insight, February 14, 2015 9:23 PM

We are naturally constrained by many natural laws in our universe.  Our governments are likewise constrained by physical laws of nature as well as the natural laws behind people, societies, economies, and ecosystems.  Where the constraints came from in nature, I don't know.  But what I do see, is that like the natural laws of the universe, societies impose other constraints upon our actions, behaviors, perceptions, chosen courses of action, abilities to frame issues and topics, abilities to define conditions within our social systems.  Governments can likewise make and define constraints for behaviors or willingness and ability to behave on the part of the citizenry, either by offering incentives to get people to behave in a particular way or to penalize and possibly limit some actions and chosen patterns of behavior. 

 

It should be noted that the laws and chosen constraints and incentives of the government on this level of existence can only be as good as the people who sit within them and make choices.  They are also limited by the physical laws of the universe and the natural laws, conditions, desires, and motives of the general public that composes the whole of society in aggregate and as that which is greater than the aggregate; the combined whole of human thought, behavior, and sentiment. 

 

These human-made constraints (created by governments and social authority figures) are also imperfect in their ability to contain and constrain the society, since the society and its members have autonomy from the government.  Humans and human societies are more constrained by the natural laws and the limitations of knowledge and perception that are present in our brains and neural systems.  Therefore, it can be said that human-made social constraints are less important than the natural ones that exist amongst ourselves and within the universe that we are apart of.

 

Therefore, I think that in order to continue to advance humanity and contribute to our potential to survive, endure, and thrive, we should be constantly and safely pushing at the constraints of what we already know and can do as individuals and as a species.  Our government(s) should focus on studying the universal natural laws of societies, economies, human behavior, and environmental functions in addition to the particular laws of their own societies, making laws and legal systems that work better and better with the natural laws of their own societies and amongst all human societies.  We should capitalize on our differences of perspective and opinion, sifting out those that don't fall into line with discovered reality while using that which is accurate to complete the puzzles of our universe in order to produce something greater than what we've presently got and to continue to advance ourselves safely and in accordance with what is actually helpful, healthful, and ethical for all sentient life in the universe.  Study, research, observation, and exploration are what will make tomorrow better than today, even as the natural laws and some conditions remain the same.  Health, well-being, quality of life, sustainability, and the ability to thrive for all are what we need to prioritize and produce as a society over financial profits and short term economic gains for a few.  Some constraints can be pushed, some can't, and some really shouldn't from the perspective of health, well-being, quality of life, and the ability to thrive for all.  Welcome to nature.

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At the Far Ends of a New Universal Law

At the Far Ends of a New Universal Law | Complexity and Biology | Scoop.it

Systems of many interacting components — be they species, integers or subatomic particles — kept producing the same statistical curve, which had become known as the Tracy-Widom distribution. This puzzling curve seemed to be the complex cousin of the familiar bell curve, or Gaussian distribution, which represents the natural variation of independent random variables like the heights of students in a classroom or their test scores. Like the Gaussian, the Tracy-Widom distribution exhibits “universality,” a mysterious phenomenon in which diverse microscopic effects give rise to the same collective behavior. “The surprise is it’s as universal as it is,” said Tracy, a professor at the University of California, Davis.

 

http://www.quantamagazine.org/20141015-at-the-far-ends-of-a-new-universal-law/


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Gary Bamford's curator insight, October 29, 2014 4:16 AM

Possibly a lesson for the 'Big Data' analytics you intent to perform, when you have the time!

Damien Thouvenin's curator insight, October 29, 2014 10:15 AM

Un article intéressant : la courbe de fréquence d'apparition d'un état dans un réseau interconnectant de nombreux éléments (de nombreux systèmes complexes donc) ne suit pas la fameuse courbe de Gauss mais plutôt celle, asymétrique, de la distribution Tracy-Widom. Le modèle a été prouvé pour un certain nombre de cas mais on ne sait pas encore identifier les critères nécessaires et suffisants à son apparition mais cela semble corroborer les effets de seuil que l'on constate dans les réseaux massivement interconnectés.

 

António F Fonseca's curator insight, November 2, 2014 6:38 AM

A new powerful law. Curiosly very similar to the profile of the quantity of retweets on Twitter.

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Complexity and the Emergence of Physical Properties

Using the effective complexity measure, proposed by M. Gell-Mann and S. Lloyd, we give a quantitative definition of an emergent property. We use several previous results and properties of this particular information measure closely related to the random features of the entity and its regularities.

 

Complexity and the Emergence of Physical Properties
Miguel Angel Fuentes

Entropy 2014, 16(8), 4489-4496; http://dx.doi.org/10.3390/e16084489


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Costas Bouyioukos's insight:

Interesting for those who look for emergent properties in biological systems!

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