Matching Items (6)

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Prebiotic RNA Network Formation: A Taxonomy of Molecular Cooperation

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Cooperation is essential for evolution of biological complexity. Recent work has shown game theoretic arguments, commonly used to model biological cooperation, can also illuminate the dynamics of chemical systems. Here

Cooperation is essential for evolution of biological complexity. Recent work has shown game theoretic arguments, commonly used to model biological cooperation, can also illuminate the dynamics of chemical systems. Here we investigate the types of cooperation possible in a real RNA system based on the Azoarcus ribozyme, by constructing a taxonomy of possible cooperative groups. We construct a computational model of this system to investigate the features of the real system promoting cooperation. We find triplet interactions among genotypes are intrinsically biased towards cooperation due to the particular distribution of catalytic rate constants measured empirically in the real system. For other distributions cooperation is less favored. We discuss implications for understanding cooperation as a driver of complexification in the origin of life.

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Created

Date Created
  • 2017-10-16

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Top-Down Causation and the Rise of Information in the Emergence of Life

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Biological systems represent a unique class of physical systems in how they process and manage information. This suggests that changes in the flow and distribution of information played a prominent

Biological systems represent a unique class of physical systems in how they process and manage information. This suggests that changes in the flow and distribution of information played a prominent role in the origin of life. Here I review and expand on an emerging conceptual framework suggesting that the origin of life may be identified as a transition in causal structure and information flow, and detail some of the implications for understanding the early stages chemical evolution.

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Created

Date Created
  • 2014-07-21

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Quantum non-barking dogs

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Quantum weak measurements with states both pre- and post-selected offer a window into a hitherto neglected sector of quantum mechanics. A class of such systems involves time dependent evolution with

Quantum weak measurements with states both pre- and post-selected offer a window into a hitherto neglected sector of quantum mechanics. A class of such systems involves time dependent evolution with transitions possible. In this paper we explore two very simple systems in this class. The first is a toy model representing the decay of an excited atom. The second is the tunneling of a particle through a barrier. The post-selection criteria are chosen as follows: at the final time, the atom remains in its initial excited state for the first example and the particle remains behind the barrier for the second. We then ask what weak values are predicted in the physical environment of the atom (to which no net energy has been transferred) and in the region beyond the barrier (to which the particle has not tunneled). Thus, just as the dog that didn't bark in Arthur Conan Doyle's story Silver Blaze gave Sherlock Holmes meaningful information about the dog's non-canine environment, here we probe whether the particle that has not decayed or has not tunneled can provide measurable information about physical changes in the environment. Previous work suggests that very large weak values might arise in these regions for long durations between pre- and post-selection times. Our calculations reveal some distinct differences between the two model systems.

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Created

Date Created
  • 2014-06-13

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Physical Universality, State-Dependent Dynamical Laws and Open-Ended Novelty

Description

A major conceptual step forward in understanding the logical architecture of living systems was advanced by von Neumann with his universal constructor, a physical device capable of self-reproduction. A necessary

A major conceptual step forward in understanding the logical architecture of living systems was advanced by von Neumann with his universal constructor, a physical device capable of self-reproduction. A necessary condition for a universal constructor to exist is that the laws of physics permit physical universality, such that any transformation (consistent with the laws of physics and availability of resources) can be caused to occur. While physical universality has been demonstrated in simple cellular automata models, so far these have not displayed a requisite feature of life—namely open-ended evolution—the explanation of which was also a prime motivator in von Neumann’s formulation of a universal constructor. Current examples of physical universality rely on reversible dynamical laws, whereas it is well-known that living processes are dissipative. Here we show that physical universality and open-ended dynamics should both be possible in irreversible dynamical systems if one entertains the possibility of state-dependent laws. We demonstrate with simple toy models how the accessibility of state space can yield open-ended trajectories, defined as trajectories that do not repeat within the expected Poincaré recurrence time and are not reproducible by an isolated system. We discuss implications for physical universality, or an approximation to it, as a foundational framework for developing a physics for life.

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Created

Date Created
  • 2017-09-01

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Formal Definitions of Unbounded Evolution and Innovation Reveal Universal Mechanisms for Open-Ended Evolution in Dynamical Systems

Description

Open-ended evolution (OEE) is relevant to a variety of biological, artificial and technological systems, but has been challenging to reproduce in silico. Most theoretical efforts focus on key aspects of

Open-ended evolution (OEE) is relevant to a variety of biological, artificial and technological systems, but has been challenging to reproduce in silico. Most theoretical efforts focus on key aspects of open-ended evolution as it appears in biology. We recast the problem as a more general one in dynamical systems theory, providing simple criteria for open-ended evolution based on two hallmark features: unbounded evolution and innovation. We define unbounded evolution as patterns that are non-repeating within the expected Poincare recurrence time of an isolated system, and innovation as trajectories not observed in isolated systems. As a case study, we implement novel variants of cellular automata (CA) where the update rules are allowed to vary with time in three alternative ways. Each is capable of generating conditions for open-ended evolution, but vary in their ability to do so. We find that state-dependent dynamics, regarded as a hallmark of life, statistically out-performs other candidate mechanisms, and is the only mechanism to produce open-ended evolution in a scalable manner, essential to the notion of ongoing evolution. This analysis suggests a new framework for unifying mechanisms for generating OEE with features distinctive to life and its artifacts, with broad applicability to biological and artificial systems.

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Created

Date Created
  • 2017-04-20

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Close Encounters of the First Kind: On Cultural Representations of Extraterrestrials, First Contact, & the Mythology of the Alien Other

Description

Western culture has oversimplified and mythologized the possibility of first contact with extraterrestrial intelligence. Whether through anthropocentrism, lack of contextual literature and/or available knowledge, or simple misunderstanding, humanity has failed

Western culture has oversimplified and mythologized the possibility of first contact with extraterrestrial intelligence. Whether through anthropocentrism, lack of contextual literature and/or available knowledge, or simple misunderstanding, humanity has failed to fully consider the impacts of seeking out alien life. Instead, humanity’s cultural and political representations of extraterrestrials tell us a great deal about the people behind the stories—all of us stuck together on our pale blue dot. This thesis explores the mythological character that is ever-present in the extraterrestrial conversation, and how past and current cultural creators in the global West have perpetuated and changed that paradigm. This thesis is also an exploration of the ways we envision our ability to contact and interact with an unknown extraterrestrial other—in many ways mythological, and in some ways as powerful symbols for struggles against oppression. I argue for a more nuanced, creative, and scientifically driven representation and consideration of first contact with extraterrestrial intelligence.

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Created

Date Created
  • 2020-12