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Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences

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https://www.readbyqxmd.com/read/29133456/the-role-of-public-goods-in-planetary-evolution
#1
REVIEW
James O McInerney, Douglas H Erwin
Biological public goods are broadly shared within an ecosystem and readily available. They appear to be widespread and may have played important roles in the history of life on Earth. Of particular importance to events in the early history of life are the roles of public goods in the merging of genomes, protein domains and even cells. We suggest that public goods facilitated the origin of the eukaryotic cell, a classic major evolutionary transition. The recognition of genomic public goods challenges advocates of a direct graph view of phylogeny, and those who deny that any useful phylogenetic signal persists in modern genomes...
December 28, 2017: Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences
https://www.readbyqxmd.com/read/29133455/how-causal-analysis-can-reveal-autonomy-in-models-of-biological-systems
#2
William Marshall, Hyunju Kim, Sara I Walker, Giulio Tononi, Larissa Albantakis
Standard techniques for studying biological systems largely focus on their dynamical or, more recently, their informational properties, usually taking either a reductionist or holistic perspective. Yet, studying only individual system elements or the dynamics of the system as a whole disregards the organizational structure of the system-whether there are subsets of elements with joint causes or effects, and whether the system is strongly integrated or composed of several loosely interacting components. Integrated information theory offers a theoretical framework to (1) investigate the compositional cause-effect structure of a system and to (2) identify causal borders of highly integrated elements comprising local maxima of intrinsic cause-effect power...
December 28, 2017: Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences
https://www.readbyqxmd.com/read/29133454/protoenzymes-the-case-of-hyperbranched-polyesters
#3
Irena Mamajanov, George D Cody
Enzymes are biopolymeric complexes that catalyse biochemical reactions and shape metabolic pathways. Enzymes usually work with small molecule cofactors that actively participate in reaction mechanisms and complex, usually globular, polymeric structures capable of specific substrate binding, encapsulation and orientation. Moreover, the globular structures of enzymes possess cavities with modulated microenvironments, facilitating the progression of reaction(s). The globular structure is ensured by long folded protein or RNA strands...
December 28, 2017: Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences
https://www.readbyqxmd.com/read/29133453/expanding-the-informational-chemistries-of-life-peptide-rna-networks
#4
REVIEW
Olga Taran, Chenrui Chen, Tolulope O Omosun, Ming-Chien Hsieh, Allisandra Rha, Jay T Goodwin, Anil K Mehta, Martha A Grover, David G Lynn
The RNA world hypothesis simplifies the complex biopolymer networks underlining the informational and metabolic needs of living systems to a single biopolymer scaffold. This simplification requires abiotic reaction cascades for the construction of RNA, and this chemistry remains the subject of active research. Here, we explore a complementary approach involving the design of dynamic peptide networks capable of amplifying encoded chemical information and setting the stage for mutualistic associations with RNA...
December 28, 2017: Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences
https://www.readbyqxmd.com/read/29133452/an-intermediate-level-of-abstraction-for-computational-systems-chemistry
#5
Jakob L Andersen, Christoph Flamm, Daniel Merkle, Peter F Stadler
Computational techniques are required for narrowing down the vast space of possibilities to plausible prebiotic scenarios, because precise information on the molecular composition, the dominant reaction chemistry and the conditions for that era are scarce. The exploration of large chemical reaction networks is a central aspect in this endeavour. While quantum chemical methods can accurately predict the structures and reactivities of small molecules, they are not efficient enough to cope with large-scale reaction systems...
December 28, 2017: Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences
https://www.readbyqxmd.com/read/29133451/chance-necessity-and-the-origins-of-life-a-physical-sciences-perspective
#6
Robert M Hazen
Earth's 4.5-billion-year history has witnessed a complex sequence of high-probability chemical and physical processes, as well as 'frozen accidents'. Most models of life's origins similarly invoke a sequence of chemical reactions and molecular self-assemblies in which both necessity and chance play important roles. Recent research adds two important insights into this discussion. First, in the context of chemical reactions, chance versus necessity is an inherently false dichotomy-a range of probabilities exists for many natural events...
December 28, 2017: Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences
https://www.readbyqxmd.com/read/29133450/resurrecting-ancestral-genes-in-bacteria-to-interpret-ancient-biosignatures
#7
Betul Kacar, Lionel Guy, Eric Smith, John Baross
Two datasets, the geologic record and the genetic content of extant organisms, provide complementary insights into the history of how key molecular components have shaped or driven global environmental and macroevolutionary trends. Changes in global physico-chemical modes over time are thought to be a consistent feature of this relationship between Earth and life, as life is thought to have been optimizing protein functions for the entirety of its approximately 3.8 billion years of history on the Earth. Organismal survival depends on how well critical genetic and metabolic components can adapt to their environments, reflecting an ability to optimize efficiently to changing conditions...
December 28, 2017: Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences
https://www.readbyqxmd.com/read/29133449/life-as-an-emergent-phenomenon-studies-from-a-large-scale-boid-simulation-and-web-data
#8
Takashi Ikegami, Yoh-Ichi Mototake, Shintaro Kobori, Mizuki Oka, Yasuhiro Hashimoto
A large group with a special structure can become the mother of emergence. We discuss this hypothesis in relation to large-scale boid simulations and web data. In the boid swarm simulations, the nucleation, organization and collapse dynamics were found to be more diverse in larger flocks than in smaller flocks. In the second analysis, large web data, consisting of shared photos with descriptive tags, tended to group together users with similar tendencies, allowing the network to develop a core-periphery structure...
December 28, 2017: Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences
https://www.readbyqxmd.com/read/29133448/origin-of-life-in-a-digital-microcosm
#9
Nitash C G, Thomas LaBar, Arend Hintze, Christoph Adami
While all organisms on Earth share a common descent, there is no consensus on whether the origin of the ancestral self-replicator was a one-off event or whether it only represented the final survivor of multiple origins. Here, we use the digital evolution system Avida to study the origin of self-replicating computer programs. By using a computational system, we avoid many of the uncertainties inherent in any biochemical system of self-replicators (while running the risk of ignoring a fundamental aspect of biochemistry)...
December 28, 2017: Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences
https://www.readbyqxmd.com/read/29133447/subsumed-complexity-abiogenesis-as-a-by-product-of-complex-energy-transduction
#10
Z R Adam, D Zubarev, M Aono, H James Cleaves
The origins of life bring into stark relief the inadequacy of our current synthesis of thermodynamic, chemical, physical and information theory to predict the conditions under which complex, living states of organic matter can arise. Origins research has traditionally proceeded under an array of implicit or explicit guiding principles in lieu of a universal formalism for abiogenesis. Within the framework of a new guiding principle for prebiotic chemistry called subsumed complexity, organic compounds are viewed as by-products of energy transduction phenomena at different scales (subatomic, atomic, molecular and polymeric) that retain energy in the form of bonds that inhibit energy from reaching the ground state...
December 28, 2017: Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences
https://www.readbyqxmd.com/read/29133446/bulk-measurements-of-messy-chemistries-are-needed-for-a-theory-of-the-origins-of-life
#11
REVIEW
Nicholas Guttenberg, Nathaniel Virgo, Kuhan Chandru, Caleb Scharf, Irena Mamajanov
A feature of many of the chemical systems plausibly involved in the origins of terrestrial life is that they are complex and messy-producing a wide range of compounds via a wide range of mechanisms. However, the fundamental behaviour of such systems is currently not well understood; we do not have the tools to make statistical predictions about such complex chemical networks. This is, in part, due to a lack of quantitative data from which such a theory could be built; specifically, functional measurements of messy chemical systems...
December 28, 2017: Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences
https://www.readbyqxmd.com/read/29133445/conceptualizing-the-origin-of-life-in-terms-of-evolution
#12
REVIEW
N Takeuchi, P Hogeweg, K Kaneko
In this opinion piece, we discuss how to place evolution in the context of origin-of-life research. Our discussion starts with a popular definition: 'life is a self-sustained chemical system capable of undergoing Darwinian evolution'. According to this definition, the origin of life is the same as the origin of evolution: evolution is the 'end' of the origin of life. This perspective, however, has a limitation, in that the ability of evolution in and of itself is insufficient to explain the origin of life as we know it, as indicated by Spiegelman's and Lincoln and Joyce's experiments...
December 28, 2017: Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences
https://www.readbyqxmd.com/read/29133444/exploring-astrobiology-using-in-silico-molecular-structure-generation
#13
REVIEW
Markus Meringer, H James Cleaves
The origin of life is typically understood as a transition from inanimate or disorganized matter to self-organized, 'animate' matter. This transition probably took place largely in the context of organic compounds, and most approaches, to date, have focused on using the organic chemical composition of modern organisms as the main guide for understanding this process. However, it has gradually come to be appreciated that biochemistry, as we know it, occupies a minute volume of the possible organic 'chemical space'...
December 28, 2017: Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences
https://www.readbyqxmd.com/read/29133443/the-thermodynamic-efficiency-of-computations-made-in-cells-across-the-range-of-life
#14
Christopher P Kempes, David Wolpert, Zachary Cohen, Juan Pérez-Mercader
Biological organisms must perform computation as they grow, reproduce and evolve. Moreover, ever since Landauer's bound was proposed, it has been known that all computation has some thermodynamic cost-and that the same computation can be achieved with greater or smaller thermodynamic cost depending on how it is implemented. Accordingly an important issue concerning the evolution of life is assessing the thermodynamic efficiency of the computations performed by organisms. This issue is interesting both from the perspective of how close life has come to maximally efficient computation (presumably under the pressure of natural selection), and from the practical perspective of what efficiencies we might hope that engineered biological computers might achieve, especially in comparison with current computational systems...
December 28, 2017: Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences
https://www.readbyqxmd.com/read/29133442/a-probabilistic-framework-for-identifying-biosignatures-using-pathway-complexity
#15
Stuart M Marshall, Alastair R G Murray, Leroy Cronin
One thing that discriminates living things from inanimate matter is their ability to generate similarly complex or non-random structures in a large abundance. From DNA sequences to folded protein structures, living cells, microbial communities and multicellular structures, the material configurations in biology can easily be distinguished from non-living material assemblies. Many complex artefacts, from ordinary bioproducts to human tools, though they are not living things, are ultimately produced by biological processes-whether those processes occur at the scale of cells or societies, they are the consequences of living systems...
December 28, 2017: Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences
https://www.readbyqxmd.com/read/29133441/universal-biology-and-the-statistical-mechanics-of-early-life
#16
Nigel Goldenfeld, Tommaso Biancalani, Farshid Jafarpour
All known life on the Earth exhibits at least two non-trivial common features: the canonical genetic code and biological homochirality, both of which emerged prior to the Last Universal Common Ancestor state. This article describes recent efforts to provide a narrative of this epoch using tools from statistical mechanics. During the emergence of self-replicating life far from equilibrium in a period of chemical evolution, minimal models of autocatalysis show that homochirality would have necessarily co-evolved along with the efficiency of early-life self-replicators...
December 28, 2017: Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences
https://www.readbyqxmd.com/read/29133440/coarse-graining-as-a-downward-causation-mechanism
#17
REVIEW
Jessica C Flack
Downward causation is the controversial idea that 'higher' levels of organization can causally influence behaviour at 'lower' levels of organization. Here I propose that we can gain traction on downward causation by being operational and examining how adaptive systems identify regularities in evolutionary or learning time and use these regularities to guide behaviour. I suggest that in many adaptive systems components collectively compute their macroscopic worlds through coarse-graining. I further suggest we move from simple feedback to downward causation when components tune behaviour in response to estimates of collectively computed macroscopic properties...
December 28, 2017: Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences
https://www.readbyqxmd.com/read/29133439/re-conceptualizing-the-origins-of-life
#18
Sara I Walker, N Packard, G D Cody
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...
December 28, 2017: Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences
https://www.readbyqxmd.com/read/29084892/a-perspective-on-quantum-integrability-in-many-body-localized-and-yang-baxter-systems
#19
Joel E Moore
Two of the most active areas in quantum many-particle dynamics involve systems with an unusually large number of conservation laws. Many-body-localized systems generalize ideas of Anderson localization by disorder to interacting systems. While localization still exists with interactions and inhibits thermalization, the interactions between conserved quantities lead to some dramatic differences from the Anderson case. Quantum integrable models such as the XXZ spin chain or Bose gas with delta-function interactions also have infinite sets of conservation laws, again leading to modifications of conventional thermalization...
December 13, 2017: Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences
https://www.readbyqxmd.com/read/29084891/thermal-inclusions-how-one-spin-can-destroy-a-many-body-localized-phase
#20
Pedro Ponte, C R Laumann, David A Huse, A Chandran
Many-body localized (MBL) systems lie outside the framework of statistical mechanics, as they fail to equilibrate under their own quantum dynamics. Even basic features of MBL systems, such as their stability to thermal inclusions and the nature of the dynamical transition to thermalizing behaviour, remain poorly understood. We study a simple central spin model to address these questions: a two-level system interacting with strength J with N≫1 localized bits subject to random fields. On increasing J, the system transitions from an MBL to a delocalized phase on the vanishing scale Jc(N)∼1/N, up to logarithmic corrections...
December 13, 2017: Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences
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