ARTICLE | doi:10.20944/preprints202007.0480.v1
Subject: Social Sciences, Geography, Planning And Development Keywords: unsustainabiliy; complex systems; holism; systemic approach; creative emergence; causal emergence; downward causation; macroscale; microscale; synergy
Online: 21 July 2020 (11:43:40 CEST)
The nature of the sustainability crisis is characterized by high levels of complexity, thus it is not amenable to be approached from the linearity or reductionist paradigm. Emergence is a multilevel phenomenon that is characterized by qualitative novelty and is recognized as an important attribute of complex systems produced by self-organized processes, unveiled from a holistic stance. This conceptual-analytical article explores the emergence phenomenon and questions whether it can be a way of enhancing the solution process to meet the sustainability challenges. Emergent properties or behaviors emerge only when the system parts interact in a wider whole. Moreover, a systemic approach is proposed as an intermediary component in the process of emergence of creative and wise solutions to the wicked problems of unsustainability. This requires observation and entails analyzing open systems as a whole and recognizing the impact of traversing macro- and micro- scales on causal and creative emergence. The study also emphasizes synergies between emergence and creativity aimed at sustainability. Sustainable development requires leapfrogging past conventional practices, in an accelerated way, and the emergence phenomenon at play between systems levels, coupled with purposefully structured creative processes, holds the potential for catalyzing sustainable development efforts.
REVIEW | doi:10.20944/preprints202211.0052.v1
Subject: Biology And Life Sciences, Virology Keywords: Monkeypox; MPXV; emergence; wild rodents; zoonoses
Online: 2 November 2022 (09:41:59 CET)
Monkeypox virus (MPXV), causing zoonotic diseases in humans, is a member of Orthopoxvirus under Poxviridae family. The virus was first reported in monkeys in 1959 in Denmark and in humans in 1970 in the Congo. Outside Africa, the virus first appeared in the USA in 2003 and since then occurred sporadically. The virus reemerged in 2017 and now spreading globally. African wild rodent mammals are thought to be the reservoir of MPXV. Exotic trade of animals and international travel favors the dissemination of MPXV. Genetic analysis shows two clades of the MPXV. Smallpox vaccine shows cross-protection and people who never in contact with Orthopoxvirus affected more than exposed ones. Fever, muscle pain, headache, and vesicle formation are the dominant clinical sign. Guarnieri-like inclusions and Ballooning degenerations are important pathognomic lesion of MPXV. It may produce case fatality rate up to 11%. Genetic materials alterations may favor the reemergence of the virus. The continuing occurrence over 73437 cases in 109 countries shows that MPXV can spread among humans competently and can be a serious issue of global public health concern. Here, we summarize the existing knowledge about re-emergence and insights into MPXV which will be of useful to curb its occurrence.
ARTICLE | doi:10.20944/preprints202209.0187.v1
Subject: Physical Sciences, Quantum Science And Technology Keywords: emergence; quantum theory; density matrix; subadditivity
Online: 14 September 2022 (03:12:07 CEST)
In this paper, we propose a quantitative definition of emergence from the density matrix framework as a state of knowledge of the system and its generalized probability formulation, in order to detect emergent properties. We propose the use of a descriptor based on the difference of von Neumann entropy, to calculate if subsystems of systems have inner correlations by defining emergent systems in terms of emergent information.
Subject: Medicine And Pharmacology, Neuroscience And Neurology Keywords: Complex systems; Emergence; Neuroimaging; Behaviour; Disorders
Online: 2 September 2020 (10:02:03 CEST)
The study of complex systems deals with emergent behaviour that arises as a result of nonlinear spatio-temporal interactions between a large number of components both within the system, as well as between the system and its environment. There is a strong case to be made that neural systems as well as their emergent behaviour and disorders, can be studied within the framework of complexity science. In particular, the field of neuroimaging has begun to apply both theoretical and experimental procedures originating in complexity science – usually in parallel with traditional methodologies. Here, we demonstrate that the use of such traditional models may distort the outcomes of neuroimaging experiments – hence affecting their interpretability and raising questions about their reliability.Therefore, we argue in favor of adopting a complex systems-based methodology in the study of neuroimaging, alongside appropriate experimental paradigms, and with minimal influences from non-complex systems approaches. Our exposition includes a review of the fundamental mathematical concepts, combined with practical examples and a compilation of results from the literature.
COMMUNICATION | doi:10.3390/sci1030024
Subject: Physical Sciences, Particle And Field Physics Keywords: elementary particle decays; emergence; power laws
Online: 13 November 2019 (00:00:00 CET)
This study analyzes the correlation between the lifetime and the rest energy of the unstable particle states with a lifetime greater than the zeptosecond (10−21 s), using data available from the Particle Data Group. This set of states seems to be divided into three groups, in each of which the two quantities can be correlated through a remarkably accurate power law. Although this fact does not represent anything new compared to the predictions of the Standard Model, it nevertheless reveals an unexpected order structure in the set of particle decays, emerging from such predictions.
ARTICLE | doi:10.20944/preprints202308.1126.v1
Subject: Physical Sciences, Quantum Science And Technology Keywords: Complexity theory, Emergence, Biology, Technology, Agency, Symmetries
Online: 16 August 2023 (11:46:46 CEST)
This paper discusses complexity theory, that is, the many theories that have been proposed for emergence of complexity from the underlying physics. Our aim is to identify which aspects have turned out to be the more fundamental ones as regards the emergence of biology, engineering, and digital computing, as opposed to those that are in fact more peripheral in these contexts. In the cases we consider, complexity arises via adaptive modular hierarchical structures that are open systems involving broken symmetries. Each emergent level is causally effective because of the meshing together of upwards and downwards causation that takes place consistently with the underlying physics. Various physical constraints limit the outcomes that can be achieved. The underlying issue concerns the origin of consciousness and agency given the basis of life in physics, which is structured starting from symmetries and variational principles with no trace of agency. A possible solution is to admit that consciousness is an irreducible emergent property of matter.
ARTICLE | doi:10.20944/preprints202308.0269.v1
Subject: Physical Sciences, Fluids And Plasmas Physics Keywords: Electric energy; cosmological inflation; emergence of conductivity
Online: 3 August 2023 (08:44:32 CEST)
Conversion of electromagnetic energy into magnetohydrodynamic energy occurs when the electric conductivity changes from negligible to finite values. This process is relevant during the epoch of reheating of the early Universe at the end of inflation and before the emergence of the radiation-dominated era. We find that conversion into kinetic and thermal energies is primarily the result of electric energy dissipation and that the magnetic energy plays only a secondary role in this process. This means that, since electric energy dominates over magnetic energy during inflation and reheating, significant amounts of electric energy can be converted into magnetohydrodynamic energy when conductivity emerges early enough, before the relevant length scales become stable.
ARTICLE | doi:10.20944/preprints202102.0299.v1
Subject: Physical Sciences, Acoustics Keywords: Emergence; Ising Model; Information; Computation; State Space
Online: 12 February 2021 (11:11:50 CET)
The exact dynamics of emergence remains one of the most prominent outstanding questions for the field of complexity science. I first discuss various perspectives on emergence in various contexts, then offer a different perspective on understanding emergence in a graph-theoretic representation. From the discussion, an observer’s choice in state space seems to have an effect for that observer to detect emergent behavior. To test these ideas, I analyze the dynamics of all possible spatial state spaces near the critical temperature in an Ising model. As a result, state space topologies that appear more deterministic flip more bits than topologies that appear more random, which is contrary to our intuitions about randomness. In addition, the size of different state spaces constrain a system’s ability to explore various states within the same time frame. These results are important to understanding emergent phenomena in biological systems, which are layered with various state spaces and observational perspectives.
REVIEW | doi:10.20944/preprints202008.0400.v1
Subject: Physical Sciences, Theoretical Physics Keywords: complex systems; emergence; complexity; chaos; fractals; networks
Online: 19 August 2020 (08:26:43 CEST)
What is a complex system? The definition of a complex system remains somewhat ambiguous. A complex system can be defined as a system consisting of many interacting parts exhibiting emergent behaviors. The emerging field of complexity science entails a change in the language of scientific research and thinking. As such, the general properties, tools and definitions pertaining to complex systems must be made accessible to multi-disciplinary systems scientists and thinkers. With this intention, this literary survey presents the development and glossary of essential concepts steering complex systems.
ARTICLE | doi:10.20944/preprints201807.0557.v1
Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: emergence; complex adaptive systems; ecosystems; biosphere; Gaia
Online: 30 July 2018 (05:11:32 CEST)
A speculative argument is presented which suggests the possible existence of a global metasystem that would be characterized as an emerging from the interaction of the units that make up the planetary system. The metasystem´s units would be the different physical, chemical and biological processes occurring in the subsystems that form the metasystem: magnetosphere, atmosphere, geosphere, hydrosphere, and biosphere. The revised global metasystem is broader than that considered in the Gaia theory or in Earth System Science, where the Earth's crust and upper atmosphere, i.e., the volume where the presence of life occurs, are considered as the limits of the system. The maintenance of the dynamic state of the global metasystem it is achieved by dissipating the free energy derived from the electromagnetic radiation of the Sun, the obtained from the Earth-Moon gravitational interaction and the energy resulting from the dynamics of the Earth core and mantle, which produces the magnetic field and much of tectonic activity. For the human species, the importance of a greater understanding of global metasystem is based on the fact that natural resources and the climate system are products of the subsystems of the global metasystem. It is possible therefore that human activities that modify the atmosphere, hydrosphere, and biosphere, change the dynamics of global metasystem.
ARTICLE | doi:10.20944/preprints202106.0019.v1
Subject: Computer Science And Mathematics, Algebra And Number Theory Keywords: algorithmic information; emergence; dynamical systems; computable systems; observers
Online: 1 June 2021 (10:38:24 CEST)
Previous work has shown that perturbation analysis in algorithmic information dynamics can uncover generative causal processes of finite objects and quantify each of its element's information contribution to computably constructing the objects. One of the challenges for defining emergence is that the dependency on the observer's previous knowledge may cause a phenomenon to present itself as emergent for one observer at the same time that reducible for another observer. Thus, in order to quantify emergence of algorithmic information in computable generative processes, perturbation analyses may inherit such a problem of the dependency on the observer's previous formal knowledge. In this sense, by formalizing the act of observing as mutual perturbations, the emergence of algorithmic information becomes invariant, minimal, and robust to information costs and distortions, while it indeed depends on the observer. Then, we demonstrate that the unbounded increase of emergent algorithmic information implies asymptotically observer-independent emergence, which eventually overcomes any formal theory that any observer might devise. In addition, we discuss weak and strong emergence and analyze the concepts of observer-dependent emergence and asymptotically observer-independent emergence found in previous definitions and models in the literature of deterministic dynamical and computable systems.
REVIEW | doi:10.20944/preprints202003.0064.v1
Subject: Biology And Life Sciences, Virology Keywords: advocacy coalition; policy; antiretroviral therapy; emergence; South Africa
Online: 4 March 2020 (10:59:44 CET)
South Africa possesses the largest anti-retroviral therapy (ART) program in the world but the path to this record was dramatic. There is scarce literature employing a comprehensive framework to explain this ART policy change and inform current policy making processes. This paper applies the Advocacy Coalition Framework (ACF) to analyse the interactions among diverse actors, institutions and networks that were associated with the ART policy change in South Africa. Post-apartheid, HIV/AIDS and AIDS-related mortality were serious public health problems. At the time, the discernible coalitions in the AIDS policy subsystem were the prescience coalition and AIDS dissidents. In view of the availability of compelling scientific evidence on the pathogenesis of HIV/AIDS, the clinical usefulness of ART, the availability of funding for national ART roll-out, strong global advocacy to reduce the cost of ART, all of these in an era when access to adequate HIV care was increasingly considered a human right, the environment to establish an appropriate ART policy for the country was conducive. However, AIDS dissidents dominated the policy agenda via their control over key institutions, the use of various dimensions of power, biasing evidence to inform policy, and promoting the activities of strong interest groups that were not in support of ART. National ART roll-out ultimately emerged as a political priority as a result of external shocks (on the ART policy subsystem) which disfavoured the dominant coalition. Failure to supplement this application of the ACF with key pubic policy concepts such as power dimensions, evidence use in policy, governance and emergence of global health networks would have led to suboptimal appraisal of the ART policy change and misinformation of current policy making processes.
REVIEW | doi:10.20944/preprints201807.0378.v1
Subject: Biology And Life Sciences, Virology Keywords: Yellow fever virus; flavivirus; vector-borne transmission, emergence
Online: 20 July 2018 (05:54:00 CEST)
As revealed by the recent resurgence of yellow fever virus (YFV) activity in the tropical regions of Africa and South America, YFV control measures need urgent rethinking. Over the last decade, most reported outbreaks occurred in, or eventually reached, areas of low vaccination coverage but suitable for virus transmission, with an unprecedented risk of expansion to densely populated territories in Africa, South America and Asia. As reflected in the World Health Organization’s initiative launched in 2017, it is high time to strengthen epidemiological surveillance to monitor accurately, viral dissemination and redefine vaccination recommendation areas. Vector-control and immunisation measures need to be adapted and vaccine manufacturing must be reconciled with an increasing demand. We will have to face more YF cases in the upcoming years hence, improving disease management through the development of efficient treatments will prove most beneficial. Undoubtedly, these developments will require in-depth descriptions of YFV biology at molecular, physiological and ecological levels. This second section of the two-part review describes the current state of knowledge and gaps regarding the molecular biology of YFV, along with an overview of the tools that can be used to manage the disease at the individual, local and global levels.
REVIEW | doi:10.20944/preprints201805.0099.v1
Subject: Biology And Life Sciences, Virology Keywords: yellow fever virus; Flavivirus; vector-borne transmission, emergence
Online: 7 May 2018 (05:19:50 CEST)
The recent resurgence of yellow fever virus (YFV) activity in the tropical regions of Africa and South America has sparked renewed interest in this infamous arboviral disease. YFV had been a human plague for centuries prior to the identification of its urban transmission vector, the Aedes aegypti mosquito species, and the development of an efficient live-attenuated vaccine, the YF-17D strain. The combination of vector-control measures and vaccination campaigns drastically reduced YFV incidence in humans on many occasions, but the virus never ceased to circulate in the forest, through its sylvatic invertebrate vector(s) and vertebrate host(s). Outbreaks recently reported in Central Africa (2015-2016) and Brazil (since late 2016), reached considerable proportions in terms of spatial distribution and total numbers of cases, with multiple exports, including to China. In turn, questions regarding the likeliness of occurrence of large urban YFV outbreaks in the Americas or of a successful import of YFV to Asia are currently resurfacing. This two-part review describes the current state of knowledge and gaps regarding the molecular biology and transmission dynamics of YFV, along with an overview of the tools that can be used to manage the disease at the individual, local and global levels.
ARTICLE | doi:10.20944/preprints202310.2014.v1
Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: biomass; Ca concentration; seedling; emergence; roots; youngest mature leaf
Online: 31 October 2023 (07:47:40 CET)
Soil sodicity is a major constraint to seedling emergence and crop production, potentially reducing plant growth due to physical and chemical constraints. Examining responses to ion imbalances may assist in the identification of genotypes tolerant to chemical constraints in sodic soils and improve productivity. We evaluated the performance of four wheat (Triticum aestivum. L) genotypes in solutions with five sodium adsorption ratios (SARs) ranging from 0 to 60. For all four genotypes, seedling emergence and shoot dry matter (DM) decreased significantly with increasing SAR. A significant positive correlation was observed between Ca concentration in roots, as well as both root and shoot DM for all genotypes. At SAR values >20, a more tolerant genotype (EGA Gregory), had higher Ca concentrations in root tissues, while a more sensitive genotype (Baxter) exhibited Na-induced Ca deficiency. Thus, selection for genotypes that are able to accumulate Ca in roots in sodic conditions may be a useful trait for selecting genotypes tolerant of soils with high ESP values. However, for soils that restrict plant growth at ESP (SAR) values of 6-10%, it is likely that growth is restricted by physical constraints rather than by a Na-induced Ca deficiency.
ARTICLE | doi:10.20944/preprints202308.0917.v1
Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: seed storage; seed viability; seedling emergence; seed ageing; germination
Online: 11 August 2023 (10:06:48 CEST)
Seed quality is crucial for the success of crop production, as it affects germination capacity, emergence potential, and seedling growth. This study investigated the impact of extended stor-age on the germination capacity, oleoresin and essential oil contents of black cumin seeds from three black cumin varieties in Ethiopia: "Aden", "Dershaye", and "Darbera". Seeds were stored for up to three years, and germination studies were conducted using a Completely Randomized De-sign. Results showed that storage period significantly affected various germination parameters, with a decrease in germination percentage observed with increasing storage period. However, variety and the interaction between storage period and variety had no statistically significant effect on germination percentage. The study also provides valuable insights into the correlations between different germination indices. Additionally, as black cumin seeds age, their oleoresin and essential oil contents decrease across all three varieties. Proper seed storage practices are essential in maintaining the germination potential of black cumin seeds, particularly over ex-tended storage periods. Overall, this study provides insights into the impact of extended seed storage on black cumin seed quality and germination potential, highlighting the importance of proper seed management practices to support sustainable crop production.
ARTICLE | doi:10.20944/preprints202005.0377.v1
Subject: Social Sciences, Language And Linguistics Keywords: narrative; meaning; emergence; subjectivity; telic aspect; global semiotics; Umwelt
Online: 23 May 2020 (16:32:04 CEST)
This theoretical paper continues a spectrum of research on sign character of narrative discourse on the background of modern post-classical theory of narrativity. It aims to uncover the relationships between the meaning of the narrative text and a sign signitication, assuming an intentional character of the narrative discourse governed by telic aspects (global semiotics). Global semiotic approach (Thomas Sebeok, 2001) views a narrative discourse as a self-organizing entity with purposeful (telic) character of all its constituent parts which turn a static text into a dynamic whole in the process of reading/perception/interpretation. The key notion for analysis of emergency is the term Umwelt (Jakob von Uexküll) to denote the perceptional world in which an organism (and a human) exists and acts as a subject. Therefore, Umwelt represents human’s perceptual boundary, which modifies the surrounding in accordance with the human’s subjective perspective. As Umwelt can be attributed to both biological and abiotic texts, meaning creation in the narrative discourse is compared to a semiotic study of comparative Umwelten (Cobley, 2014) where narrative is defined as a modeling device for the world creation through embodied subjectivity. It has been confirmed, that stressing on the subjective sphere of information eхchange and processing from the position of global semiotics necessitates introduction of basic principles of biosemiotics (i.e. semiotic scaffolding etc.) and teleology (i.e. cause, purpose, result) to analysis of narrative discourse and it constitutes the perspectives for further research in this domain.
ARTICLE | doi:10.20944/preprints202109.0327.v1
Subject: Physical Sciences, Thermodynamics Keywords: heat equation; relativistic heat equation; emergence of entropy; equipartition theorem
Online: 20 September 2021 (11:05:37 CEST)
Motivated by the well-known contradiction of special relativity and the heat equation, a wave equation for temperature scalar field is presented that also resolves the old controversy of (Lorentz) transformation of temperature and entropy. After showing that the current dogma of temperature and entropy being emergent concepts is based on but a logical fallacy, it is proposed that single particles posses entropy. This principle of fundamentality of entropy is then shown to be compatible with the equipartition theorem by yielding corrections in the quantum gravity regime.
ARTICLE | doi:10.20944/preprints202107.0692.v1
Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: Lyme disease; Quebec; Spatiotemporal patterns; front wave velocity; clusters; emergence
Online: 30 July 2021 (09:38:26 CEST)
Lyme disease is a growing public health problem in Québec. Its emergence over the last decade is caused by environmental and anthropological factors that favour the survival of Ixodes scapularis, the vector of Lyme disease transmission. The objective of this study was to estimate the speed and direction of Lyme disease emergence in Québec and to identify spatiotemporal risk patterns. A surface trend analysis was conducted to estimate the speed and direction of its emergence based upon the first detected case of Lyme disease in each municipality in Québec since 2004. A cluster analysis was also conducted to identify at-risk regions across space and time. These analyses were reproduced for the date of disease onset and date of notification for each case of Lyme disease. It was estimated that Lyme disease is spreading northward in Québec at a speed varying between 18 and 32 km/year according to the date of notification and the date of disease onset, respectively. A high rate of disease risk was found in seven clusters identified in the south-west of Québec in the sociosanitary regions of Montérégie and Estrie. The results obtained in this study improve our understanding of the spatiotemporal patterns of Lyme disease in Québec, which can be used for proactive, targeted interventions by public and clinical health authorities.
ARTICLE | doi:10.20944/preprints202009.0035.v1
Subject: Medicine And Pharmacology, Pathology And Pathobiology Keywords: enterovirus; nonhuman primates; humans; genetic recombination; emergence; Republic of Congo
Online: 2 September 2020 (08:49:42 CEST)
Enteroviruses (EVs) are viruses of the family Picornaviridae that cause mild to severe infections in humans and in several animal species, including nonhuman primates (NHPs). We conducted a survey and characterization of enteroviruses circulating between humans and great apes in the Congo. Fecal samples (N=24) of gorillas and chimpanzees living close to or distant from humans in three Congolese parks were collected, as well as from healthy humans (N=38) living around and within these parks. Enterovirus were detected in 29.4% gorilla and 13.15% human feces, including wild and human-habituated gorillas, local humans and eco-guards. Two identical strains were isolated from two humans come from two remote regions. Their genomes were similar and all genes showed their close similarity to Coxsackieviruses except for 3C, 3D and 5’UTR region where they were most similar to poliovirus 1 and 2, suggesting recombination. Recombination events were found between these strains, poliovirus 1 and 2 and EV-C99. The same EV- C species detected in both humans and apes in different regions suggest a clonal distribution of the virus in Congo.
REVIEW | doi:10.20944/preprints202212.0002.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Emergence of Life; Hydrothermal vents; Electrotrophy; Prebiotic synthesis; Electroreduction of CO2
Online: 1 December 2022 (01:06:47 CET)
The emergence of Life has been a subject of intensive research for decades. Different approaches and different environmental “cradles” have been studied, from space to the deep-sea. Since the recent discovery of a natural electrical current through the deep-sea hydrothermal vent, a new energy source is considered for the transition from inorganic to organic. This energy source is used by modern microorganisms using a new trophic type, called electrotrophy. In this review, we draw the parallel between this metabolism and a new theory for the emergence of Life based on this electrical electron flow. Each step of the creation of Life is revised in the new light of this prebiotic electrochemical context, going from the evaluation of similar electrical current during the Hadean, the CO electroreduction into a prebiotic primordial soup, the production of proto-membranes, the energetic system inspired of the nitrate reduction, the proton gradient, and the transition to a planktonic proto-cell. Finally, this theory is compared to the two other theories in hydrothermal context, to assess its relevance to overcome the limitations of each one. Many critical factors that were limiting each theory can be overcome with the effect of the electrochemical reactions and the environmental changes produced.
ARTICLE | doi:10.20944/preprints202101.0165.v1
Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: base temperature; base water potential; predictive weed emergence model; weed germination
Online: 8 January 2021 (14:12:28 CET)
The efficacy of weed management depends on the correct control timing according to the seedling emergence dynamics. Since soil temperature and soil moisture are two main factors that determine weed germination, the hydrothermal time model can be used to predict their emergence. The aim of this study was to estimate the base temperature (Tb) and base water potential (Ψb) for germination of Chenopodium album, Amaranthus retroflexus, Setaria pumila and Panicum capillare collected from fields in continental Croatia and then to compare these values with those of Italian populations embedded in the AlertInf model. Germination tests were performed at seven constant temperatures (ranging from 4 to 27°C) and eight water potentials (0.00 to - 1.00 MPa). Estimated Tb and Ψb were 3.4°C, -1.38 MPa for C. album, 13.9°C, -0.36 MPa for A. retroflexus, 6.6°C, -0.71 MPa for S. pumila and 11.0°C, -0.87 MPa for P. capillare, respectively. According to the criterion of overlap of the 95% confidence intervals, only Tb of C. album, and Ψb of A. retroflexus were similar between Croatian and Italian populations. Further field experiments should be conducted in the Croatian field to monitor weed emergence patterns of C. album and to calibrate the AlerInf equation parameters.
HYPOTHESIS | doi:10.3390/sci2030073
Subject: Arts And Humanities, Humanities Keywords: emergence of life; game of life; inefficiency objection; simpson’s paradox; astrobiology
Online: 18 September 2020 (00:00:00 CEST)
We address the need for a model by considering two competing theories regarding the origin of life: (i) the Metabolism First theory and (ii) the RNA World theory. We discuss two inter-related points. (I) Models are valuable tools in understanding both the processes and intricacies of the origin of life issues. (II) Insights from models also help us to evaluate the core objection to origin of life theories called “the inefficiency objection” commonly raised by proponents of both the Metabolism First theory and the RNA World theory against each other. We use Simpson’s paradox as a tool for challenging this objection. We will use models in various senses ranging from taking them as representations of reality to treating them as theories/accounts that provide heuristics for probing reality. In this paper, we will frequently use models and theories interchangeably. Additionally, we investigate Conway’s Game of Life and contrast it with our Simpson’s Paradox (SP)-based approach to emergence of life issues. Finally, we discuss some of the consequences of our view. A scientific model is testable in three senses: (i) a logical sense, (ii) a nomological sense, and (iii) a current technological sense. The SP-based model is testable in the logical sense. It is also testable nomologically. However, it is not currently feasible to test it.
ARTICLE | doi:10.20944/preprints201912.0227.v1
Subject: Physical Sciences, Mathematical Physics Keywords: information; process; process algebra; causal tapestry; process tapestry; transience; contextuality; emergence
Online: 17 December 2019 (10:07:58 CET)
The Process Algebra model has been shown to provide an alternative mathematical framework for non-relativistic quantum mechanics (NRQM). It reproduces the wave functions of non-relativistic quantum mechanics to a high degree of accuracy. It posits a fundamental level of finite, discrete events upon which the usual entities of NRQM supervene. It has been suggested that the Process Algebra model provides a true completion of NRQM, free of divergences and paradoxes, with causally local information propagation, contextuality and realism. Arguments in support of these claims have been mathematical. Missing has been an ontology of this fundamental level from which the formalism naturally emerges. In this paper it is argued that information and information flow provides this ontology. Higher level constructs such as energy, momentum, mass, spacetime, are all emergent from this fundamental level.
ARTICLE | doi:10.20944/preprints201912.0019.v1
Subject: Physical Sciences, Quantum Science And Technology Keywords: identical quantum particles; indistinguishability; the concept of a particle; emergence; entanglement
Online: 3 December 2019 (05:59:55 CET)
Particles in classical physics are distinguishable objects, which can be picked out individually on the basis of their unique physical properties. By contrast, in quantum mechanics the standard view is that particles of the same kind (``identical particles'') are completely indistinguishable from each other. This standard view is problematic: Particle indistinguishability is irreconcilable not only with the very meaning of ``particle'' in ordinary language and in classical physical theory, but also with how this term is used in the practice of present-day physics. Moreover, the indistinguishability doctrine prevents a smooth transition from quantum particles to what we normally understand by ``particles'' in the classical limit of quantum mechanics. Elaborating on earlier work, we here discuss an alternative to the standard view that avoids these and similar problems. As it turns out, this alternative approach connects to recent discussions in quantum information theory concerning the question of when identical particles can be considered to be entangled.
ARTICLE | doi:10.20944/preprints202308.0164.v1
Subject: Social Sciences, Cognitive Science Keywords: Emergence; Information; Consciousness; Integrated Information Theory; Emergent Information Theory; Connectome; Artificial Intelligence
Online: 2 August 2023 (08:36:05 CEST)
In spite of its remarkable characteristics, consciousness cannot be considered in splendid isolation. It is only one of the remarkable phenomena associated with the brain, the brain is just one of the organs in the body, and computers and brains share many characteristics as information-based systems. On the basis of the ubiquitous hierarchical organization of reality into stacked layers, and the particular importance of strong emergence in living systems, this article argues that the brain must also employ such methods to achieve its advanced functions. This is in line with the prop-osition of Integrated Information Theory (IIT) that consciousness requires a high degree of causal integration in its physical substrate. However, such emergence is also shown to underlie infor-mation processing in computers and the non-conscious functions of the brain. It is also demon-strated that both computers and brains exploit a specific type of information that is correlated to but not synonymous with states and mechanisms in the physical substrate. Emergent Information Theory (EIT) therefore presents consciousness as one member of a large and diverse family of non-physical but real forms of emergent information created by specific types of designed and evolved systems.
ARTICLE | doi:10.20944/preprints202111.0359.v2
Subject: Physical Sciences, Particle And Field Physics Keywords: Quantum Gravity; Problem of Time; Particle Physics; Emergence; Holographic Principle; Model Sets
Online: 23 March 2022 (09:26:42 CET)
We consider partition functions, in the form of state sums, and associated probabilistic measures for aperiodic substrates described by model sets and their associated tiling spaces. We propose model set tiling spaces as microscopic models for small scales in the context of quantum gravity. Model sets possess special self-similarity properties that allow us to consider implications on large and observable scales from the underlying (non-ergodic) dynamics. In particular we consider the implication of the underlying aperiodic substrate for the well known problem of time in quantum gravity, and propose a correspondence between small and large scales, the so-called ergodic correspondence, that addresses the emergence of matter properties and spacetime structure. In the process we find a possible bound in the mass spectrum of fundamental particles.
ARTICLE | doi:10.20944/preprints201703.0171.v1
Subject: Computer Science And Mathematics, Mathematics Keywords: identity over time; Bayesian networks; multi-information; entity; persistence; integration; emergence; naturalising agency
Online: 21 March 2017 (16:23:00 CET)
We present a first formal analysis of specific and complete local integration. Complete local integration was previously proposed as a criterion for detecting entities or wholes in distributed dynamical systems. Such entities in turn were conceived to form the basis of a theory of emergence of agents within dynamical systems. Here, we give a more thorough account of the underlying formal measures. The main contribution is the disintegration theorem which reveals a special role of completely locally integrated patterns (what we call ι-entities) within the trajectories they occur in. Apart from proving this theorem we introduce the disintegration hierarchy and its refinement-free version as a way to structure the patterns in a trajectory. Furthermore we construct the least upper bound and provide a candidate for the greatest lower bound of specific local integration. Finally, we calculate the i-entities in small example systems as a first sanity check and find that ι-entities largely fulfil simple expectations.
ARTICLE | doi:10.20944/preprints202304.0486.v1
Subject: Engineering, Chemical Engineering Keywords: Ultrasound irradiation; Liquid protrusion; Beads fountain/column/jet; Mist emergence; Acoustic conditions; Visual analysis
Online: 18 April 2023 (04:56:45 CEST)
The process of ultrasonic atomization involves a series of dynamic/topological deformations of free surface, though not always, of a bulk liquid (initially) below the air. This study focuses on such dynamic interfacial alterations realized by changing some acousto-related operating conditions, including ultrasound excitation frequency, acoustic strength or input power density, and the presence/absence of a “stabilizing” nozzle. High-speed, high-resolution imaging made it possible to qualitatively identify four representative transitions/demarcations: 1) the onset of a protrusion on otherwise flat free surface; 2) the appearance of undulation along the growing protuberance; 3) the triggering of emanating beads fountain out of this foundation-like region; and 4) the induction of droplets bursting and/or mist spreading. Quantitatively examined were the two-parameters specifications—on the degrees as well as induction—of the periodicity in the protrusion-surface and beads-fountain oscillations, detected over wider ranges of driving/excitation frequency (0.43–3.0 MHz) and input power density (0.5–10 W/cm2) applied to the ultrasound transducer of flat surface on which the nozzle was mounted or not. The resulting time sequence of images processed for the extended operating ranges, regarding the fountain structure pertaining in particular to recurring beads, confirms the wave-associated nature, i.e., their size “scalability” to the ultrasound wavelength, predictable from the traveling wave relationship. The thresholds in acoustic conditions for each of the four transition states of the fountain structure have been identified—notably, the onset of plausible “bifurcation” in the chain-beads diameter below a critical excitation frequency.
REVIEW | doi:10.20944/preprints202207.0250.v1
Subject: Biology And Life Sciences, Virology Keywords: Emergence of Omicron and its mechanism; mutation and sub-lineages; Monoclonal antibodies; Antiviral drugs
Online: 18 July 2022 (07:48:00 CEST)
With the ongoing COVID pandemic, the emergence of a novel omicron variant in November 2021 has chaos the world. Despite mass vaccination, this omicron has spread rapidly raising concerns around the globe. The Omicron variant has a vast array of mutations as compared to another variant of concern with overall 50 mutations where 30 mutations are present in its spike protein. This mutation has led to immune escape and more transmissibility compared to other variants, including Delta. A cluster of mutations (H655Y, N679K, and P681H) present at the omicron spike protein could aid in transmission. Currently, no virus-specific data are available to predict the efficacy of anti-viral and mAbs drugs. However, two monoclonal antibody drugs: Sotrovimab and Evusheld are authorized for emergency use in COVID patients. This virus is not fading away soon. The easiest solution and less expensive measure to fight against this pandemic are following COVID appropriate protocols.There is need to strengthen the level of research for development of potential vaccines and anti-viral drugs. It is also important to monitor and expand genomic surveillance to keep track of the emergence of new variants thus avoiding the spread of new diseases worldwide. This article highlights the emergence of omicron and vast number of mutation in its protein. In addition, recent advancement in drugs approved by FDA to treat COVID patients has been listed and focused in this paper.
REVIEW | doi:10.20944/preprints202106.0204.v1
Subject: Public Health And Healthcare, Public, Environmental And Occupational Health Keywords: One Health; Planetary Health; Pandemics; Ecology; Evolution; Environment; Climate change; Biodiversity loss; Emergence; Pathogen
Online: 8 June 2021 (09:34:57 CEST)
The implementation of One Health/EcoHealth/Planetary Health approaches has been identified as key (i) to address the strong interconnections between risk for pandemics, climate change and biodiversity loss, and (ii) to develop and implement solutions to these interlinked crises. As a response to the multiple calls of scientists in that direction, we have put forward seven long term research questions regarding COVID-19 and emerging infectious diseases (EIDs) that are based on an effective integration of environmental, ecological, evolutionary, and social sciences to better anticipate and mitigate EIDs. Research needs cover the social-ecology of infectious disease agents, their evolution, the determinants of susceptibility of humans and animals to infections, and the human and ecological factors accelerating infectious disease emergence. For comprehensive investigation, they include the development of nature-based solutions to interlinked global planetary crises, addressing ethical and philosophical questions regarding the relationship of humans to nature and regarding transformative changes to safeguard the environment and human health. In support of this research, we propose the implementation of innovative multidisciplinary facilities embedded in social-ecosystems locally: the “ecological health observatories” and the “living laboratories”. This work has been carried out in the frame of the EC project HERA (www.HERAresearchEU.eu) that aims to set the priorities for an environment, climate and health research agenda in the EU by adopting a systemic approach in the face of global environmental change.
ARTICLE | doi:10.20944/preprints201608.0163.v1
Subject: Computer Science And Mathematics, Computer Science Keywords: emergence; uniqueness; existence of solutions; input/output system; system specifications; discrete event system specification
Online: 17 August 2016 (11:29:23 CEST)
Conditions under which compositions of component systems form a well-defined system-of-systems here are formulated at a fundamental level. Statement of what defines a well-defined composition and sufficient conditions guaranteeing such a result offers insight into exemplars that can be found in special cases such as differential equation and discrete event systems. For any given global state of a composition, two requirements can be stated informally as: 1) the system can leave this state, i.e., there is at least one trajectory defined that starts from the state, and 2) the trajectory evolves over time without getting stuck at a point in time. Considered for every global state, these conditions determine whether the resultant is a well-defined system and if so, whether it is non-deterministic or deterministic. We formulate these questions within the framework of iterative specifications for mathematical system models that are shown to be behaviorally equivalent to the Discrete Event System Specification (DEVS) formalism. This formalization supports definitions and proofs of the afore-mentioned conditions. Implications are drawn at the fundamental level of existence where the emergence of a system from an assemblage of components can be characterized. We focus on systems with feedback coupling where existence and uniqueness of solutions is problematic.
Subject: Physical Sciences, Theoretical Physics Keywords: self-simulation hypothesis; principle of efficient language; quasicrystals; game of life; emergence; state sum models
Online: 9 September 2021 (11:08:57 CEST)
In light of the self-simulation hypothesis, a simple form implementation of the principle of efficient language is discussed in a self-referential geometric quasicrystalline state sum model in three dimensions. Emergence is discussed in context of geometric state sum models.
ARTICLE | doi:10.20944/preprints202308.0793.v1
Subject: Computer Science And Mathematics, Artificial Intelligence And Machine Learning Keywords: edge computing; human vocalization; emergence vehicle siren; EfficientNet-based; fuzzy rank-based ensemble model; hearing impairment.
Online: 9 August 2023 (15:18:17 CEST)
Wearable assistant devices play an important role in daily life for people with disabilities. Those who are hearing impaired may face dangers while walking or driving on the road. The major danger is their inability to hear warning sounds from cars or ambulances. Thus, the goal of this study is to develop a wearable assistant device for the hearing impaired to recognize emergency vehicle sirens on the road using edge computing. An EfficientNet-based fuzzy rank-based ensemble model was proposed to classify seven audio sounds, including human vocalizations and emergency vehicle sirens. This model was embedded in an Arduino Nano 33 BLE Sense development board. The audio files were respectively obtained from the CREMA-D dataset and Large Scale Audio dataset of emergency vehicle sirens on the road, with a total number of 8756 files. The seven audio sounds included neutral vocalization, anger vocalization, fear vocalization, happy vocalization, car horn sound, siren sound, and ambulance siren sound. The audio signal was converted into a spectrogram by the short-time Fourier transform as the feature. When one of the car horns, sirens, or ambulance sirens was detected, the wearable assistant device presented alarms through vibration and messages on the OLED panel. The performances of the EfficientNet-based fuzzy rank-based ensemble model in offline computing achieved an accuracy of 97.1%, precision of 97.79%, sensitivity of 96.8%, and specificity of 97.04%. In edge computing, the results were an accuracy of 95.2%, precision of 93.2%, sensitivity of 95.3%, and specificity of 95.1%. Thus, the proposed wearable assistant device has the potential benefit of helping the hearing impaired avoid traffic accidents.
ARTICLE | doi:10.20944/preprints201808.0096.v1
Subject: Environmental And Earth Sciences, Geography Keywords: Hadean; carbonic ocean; mantle plumes; Banded Iron Formation; green rust; submarine alkaline vents; emergence of life
Online: 6 August 2018 (05:19:46 CEST)
Korenaga and coworkers present evidence to suggest that 4.3 billion years ago the Earth’s mantle was dry and water filled the ocean to twice its present volume. CO2 was constantly exhaled during the mafic to ultramafic volcanic activity associated with magmatic plumes that produced the thick, dense and relatively stable oceanic crust. In that setting two distinct major types of sub-marine hydrothermal vents were active: ~400 °C acidic springs whose effluents bore vast quantities of iron into the ocean, and ~120 °C, highly alkaline and reduced vents exhaling from the cooler, serpentinizing crust at some distance from the heads of the plumes. When encountering the alkaline effluents, the iron from the plume head vents precipitated out forming mounds likely surrounded by voluminous exhalative deposits similar to the banded iron formations known from the Archean. These mounds and the surrounding sediments likely comprising nanocrysts of the variable valence FeII/FeIII oxyhydroxide, green rust. The precipitation of green rust, along with subsidiary iron sulfides and minor concentrations of Ni, Co and Mo in the environment at the alkaline springs may have established both the key bio-syntonic disequilibria, and the means to properly make use of them – those needed to drive the essential inanimate-to-animate transitions that launched life. In the submarine alkaline vent model for the emergence of life specifically it is first suggested that the redox-flexible green rust microcrysts spontaneously formed precipitated barriers to the complete mixing of carbonic ocean and alkaline hydrothermal fluids, barriers that created and maintained steep ionic disequilibria; and second, that the hydrous interlayers of green rust acted as 'engines' that were powered by those ionic disequilibria and drove essential endergonic reactions. There, aided by sulfides and trace elements acting as catalytic promoters and electron transfer agents, nitrate could be reduced to ammonia and carbon dioxide to formate, while methane may have been oxidized to methyl and formyl groups. Acetate and higher carboxylic acids could then have been produced from these C1 molecules and aminated to amino acids, and thence oligomerized to offer peptide nests to phosphate and iron sulfides and secreted to form primitive amyloid-bounded structures, leading conceivably to protocells.
ARTICLE | doi:10.20944/preprints202010.0505.v1
Subject: Social Sciences, Area Studies Keywords: Sharing Economy; Category Formation; Emergence; Social Movement; Similarity Clustering; Truce; Radial Category; Identity Legitimation; Stakeholders; Business Models.
Online: 26 October 2020 (08:50:38 CET)
The Sharing Economy (SE) has dawn great attention from several stakeholders in society in the last five years. While business actors are interested in financial opportunities to meet consumer needs, new business models, the academia and governmental organizations are concerned with potential unintended effects on the society and environment. In the process of making a clearer comprehension of the SE phenomenon, researchers have identified that, despite its notable global growth, there still persists a lack of a more solid ground in understanding its origins and respective mechanisms under which it has been evolving over time as a category. In this research, we address the problematics of the origins and ascendency of the SE by examining the process by which the SE is arising as a new category, searching for conceptual clarification and pinpointing the legitimacy granted by key stakeholders. Our guiding research questions are: (1) how the SE was formed and evolved as a market category; and (2), as a market category, is the SE legitimate? Additionally, we attempt to identify the nature of the SE as a category. To answer these questions, we conducted an historical analysis of the expression SE and its equivalents. This paper deepens the discussion about the nature of the SE by providing evidence that (i) the SE has predominantly been formed by emergence processes, comprising social movement, similarity clustering and truce components. It is the combination of all these aforementioned processes that renders the SE a special case of market category formation, which, in turn, has been allowing communication, entrepreneurship, regulation and research about what really is the SE, and despite the evident lack of agreements regarding both the label and its content; (ii) there is a generalized legitimacy granted to the SE by a vast number of stakeholders, even though still lacking on the consolidation of socio-political legitimation, and (iii) the nature of the SE seems to fall in a metaphorical approach, particularly, the notion of radial categories.
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: zoonotic risk; viral emergence; viral ecology; genomics; machine learning; access and benefit sharing; intellectual property law; global health
Online: 7 April 2021 (11:53:59 CEST)
In light of the urgency raised by the COVID-19 pandemic, global investment in wildlife virology is likely to increase, and new surveillance programs will identify hundreds of novel viruses that might someday pose a threat to humans. Our capacity to identify which viruses are capable of zoonotic emergence depends on the existence of a technology—a machine learning model or other informatic system—that leverages available data on known zoonoses to identify which animal pathogens could someday pose a threat to global health. We synthesize the findings of an interdisciplinary workshop on zoonotic risk technologies to answer the following questions: What are the prerequisites, in terms of open data, equity, and interdisciplinary collaboration, to the development and application of those tools? What effect could the technology have on global health? Who would control that technology, who would have access to it, and who would benefit from it? Would it improve pandemic prevention? Could it create new challenges?
ARTICLE | doi:10.20944/preprints201810.0736.v1
Subject: Computer Science And Mathematics, Artificial Intelligence And Machine Learning Keywords: Artificial Intelligence (AI); artificial general intelligence (AGI); artificial social intelligence (ASI); singularity; complexity; emergence phenomena; evolution; social sciences
Online: 31 October 2018 (07:45:49 CET)
In this paper we present an argument in favor of the possibility of an artificial intelligence above human intelligence. AI technology has shown a stepwise increase in its capacity and complexity. The last step took place several years ago, due to increased progress in deep neural network technology. Each such step goes hand in hand with our understanding of ourselves, understanding human cognition. Indeed, AI was always about the question of understanding human nature. AI percolates into our lives, step by step, changing our environment. We believe the next few steps in AI technology, and in our understanding of human behavior, will bring about a much more powerful machines, flexible enough to resemble human behavior. In this context, there are two research fields: Artificial Social Intelligence (ASI) and General Artificial Intelligence (AGI). On the ground of ASI and AGI we present an evolutionary argument which uses research in artificial life simulations, showing an increase in complexity due to an emergent property coming out of lower complexity constituents. The whole process is driven by an evolutionary force. What could such an evolutionary force be? We suggest a social communicative driving force. We end the discussion demonstrating a way to overcome our fears of singularity, harnessing value alignment.
REVIEW | doi:10.20944/preprints202005.0058.v1
Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: synthetic biology; multi-agent modelling; individual-based modelling; agent-based modelling; systems biology; emergence; multi-scale; bioengineering; consortia; collectives
Online: 5 May 2020 (03:45:16 CEST)
Many complex behaviours in biological systems emerge from large populations of interacting molecules or cells, generating functions that go beyond the capabilities of the individual parts. Such collective phenomena are of great interest to bioengineers due to their robustness and scalability. However, engineering emergent collective functions is difficult because they arise as a consequence of complex multi-level feedback, which often spans multiple length-scales. Here, we present a perspective on how some of these challenges could be overcome by using multi-agent modelling as a design framework within synthetic biology. Using case studies covering the construction of synthetic ecologies to biological computation and synthetic cellularity, we show how multi-agent modelling can capture the core features of complex multi-scale systems and provide novel insights into the underlying mechanisms which guide emergent functionalities across scales. The ability to unravel design rules underpinning these behaviours offers a means to take synthetic biology beyond single molecules or cells and towards the creation of systems with functions that can only emerge from collectives at multiple scales.
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: protein/rna world; plasma membrane; cytoplasm; virus world; pre-retro virus; emergence of dna; transcription and replication; first cells; hyperthermophiles; luca; bacteria and archaea; anoxygenic bacteria; oxygenic bacteria; global distribution of cyanobacteria
Online: 15 October 2019 (11:18:58 CEST)
The transition from the Peptide/RNA world to the Protein/RNA world in the hydrothermal vent environment was a major event in the history of life. The advent of proteins utterly changed the conditions of emerging life, representing a watershed in its development. During subsequent translation various protein enzymes emerged driving protocells into a more complex and interconnected system. With their astonishing versatility, the protein enzymes catalyzed crucial biochemical reactions within protocells into more complex biomolecules in diverse metabolic pathways, whereas structural proteins provided strength and permeability in the cell membrane. Four major events followed after availability of various kinds of protein molecules during prebiotic synthesis. These are: (1) the modification of the phospholipid membrane into the plasma membrane; (2) the origin of primitive cytoplasm; (3) the beginnings of the virus world; and (4) the advent of DNA. The first innovation mediated by proteins was the improvement of the cell membrane. The phospholipid membrane was initially evolved in a vent environment from the gradual modification of a fatty acid membrane via an intermediate phosphatidate acid by non-enzymatic reactions. The phospholipid is then synthesized from phosphatidate acid by a series of enzymes. To make the phospholipid membrane more permeable, various protein molecules interacted with the cell membrane. Proteins not only stabilized the wall membrane, but also acted as pumps, preventing some molecules from the protocells from crossing the membrane barriers, while permitting other selected molecules and ions to enter and leave the protocell. The second modification led by proteins is the gradual conversion of the interior of the protocell from a water-like medium into a gel-like cytoplasm, which became the storehouse of a wide range of biomolecules including amino acids, proteins, nucleic acids, ribosomes, as well as salt and water. The third innovation utilizing the newly synthesized proteins was the emergence of the ancient virus world. In the milieu of different kinds of mRNAs in the prebiotic soup, jelly-roll capsid genes originated de novo within genomes of nonviral mRNAs by overprinting. These fragile capsid genes were possibly coated by proteins on the mineral substrate for stability and durability, transforming them into ancient viral particles. These protein coats were random and were not encoded by encased genes. Some protocells might have engulfed these viral particles, when the capsid genes utilized the ribosomes of the host to translate into the appropriate capsid proteins. These capsid proteins then coated the viral genes to make new copies of primordial viruses inside the protocell. Since then, viruses became capsid-encoding organisms. These primordial mRNA viruses parasitized RNA-based protocells, manipulating them to make new copies of themselves. This was the beginning of a relentless war between viruses and their protocellular hosts. The next stage in viral evolution was the emergence of a primitive retrovirus (pre-retrovirus) with a new kind of replicative strategy in a sense that it could turn its RNA into DNA using its own reverse transcriptase enzyme. This is the beginning of the Retro world that facilitated the transition from RNA to DNA genomes. The infection of RNA protocells with pre-retroviruses progressively transferred the RNA genome to a viral DNA genome by retro-transcription. The advent of DNA by the pre-retrovirus marks the fourth innovation, when a number of enzymes had already developed and were utilized by pre-retroviruses. With continued infection, DNA viruses slowly transferred not only their core replication enzymes, such as helicase, primase, and DNA polymerase, to RNA protocells, but also to their DNAs as well. Thus, began the DNA world, when DNA replaced RNA as the major genome of the protocells. With the advent of DNA, replication of information was entirely dissociated from its expression. Because DNA is much more stable than mRNA with more storage capacity, it is a superb archive for information systems in the form of base sequences. DNA progressively took over the replicative storage function of mRNA, leaving the latter for protein synthesis. The new protocell with the DNA genome will diversify into large populations of DNA protocells that will outcompete populations of RNA protocells. Genetic information began to flow from DNA to mRNA to protein in a two-step process involving transcription and translation. In the biological stage, DNA replication was central to the binary fission of the first cell, orchestrated by the duplication of genomes and then the division of the parent cell into two identical daughter cells. It was carried out by a set of enzymes that formed a Z-ring at the site of replication. With the onset of binary fission, the population of primitive cells grew rapidly in the hydrothermal vent environment, undergoing Darwinian evolution and diversification. These primordial hyperthermophiles, presumably the first life, obtained food and energy directly from the vent environment. However, such a situation was self-limiting, so the early cells evolved their own mechanisms for generating metabolic energy and synthesizing the molecules necessary for their reproduction. The earliest fossil record (≥ 3.5 Ga) of biotic activity is preserved in the Archean hydrothermal and sedimentary rocks of the Nuvvuagittuq Craton of Canada, the Isua Craton of Greenland, the Pilbara Craton of Australia, the Kaapvaal Craton of South Africa, and the Singhbhum Craton of India in the form of the carbonaceous remains of microbial cells, cellular microfossils, and stromatolites. These microscopic fossils provide crucial evidence of the origin and early evolution of prokaryotic cells, beginning with hyperthermophiles. Molecular phylogenetic analysis suggests that both domains of life ¬– Bacteria and Archaea probably split from the last universal common ancestor (LUCA), a hyperthermophilic organism. In the younger sequences of these Archean cratons, two kinds of photosynthetic bacteria, anoxygenic green sulfur bacteria, and oxygenic cyanobacteria, appeared in quick succession from the thermophilic ancestor, indicating a shift of niche from a benthic to a planktonic, with reduced thermotolerance. The development of anoxygenic and oxygenic photosynthesis would have allowed life to escape the hydrothermal setting and invade a newly evolved habitat—broad continental shelves to tap solar energy. Cyanobacteria invaded the global ocean, turned it into blue and green, produced oxygen for the first time, and left their signatures in the carbonates and stromatolites.
Subject: Environmental And Earth Sciences, Paleontology Keywords: protein/RNA world: plasma membrane; cytoplasm; gene regulation; virus world; pre-retro virus; emergence of DNA; transcription and replication; first cells; hyperthermophiles; LUCA; Bacteria and Archaea; anoxygenic bacteria; oxygenic bacteria; global distribution of cyanobacteria
Online: 12 February 2020 (03:25:07 CET)
The emergence of proteins in the prebiotic world was a watershed event at the origin of life. With their astonishing versatility, the protein enzymes catalyzed crucial biochemical reactions within protocells into more complex biomolecules in diverse metabolic pathways, whereas structural proteins provided strength and permeability in the cell membrane. Five major biochemical innovations followed in succession after availability of various kinds of protein molecules during decoding and translation of mRNAs. These are: (1) the modification of the phospholipid membrane into the plasma membrane; (2) the origin of primitive cytoplasm; (3) primitive gene regulation; (4) the beginnings of the virus world; and (5) the advent of DNA. The creative role of viruses during prebiotic synthesis led to the origin of the DNA world, when DNA replaced mRNA as the major genome of the protocells. With the advent of DNA, replication of information was entirely dissociated from its expression. Because DNA is much more stable than mRNA with more storage capacity, it is a superb archive for information systems in the form of base sequences. DNA progressively took over the replicative storage function of mRNA, leaving the latter for protein synthesis. Genetic information began to flow from DNA to mRNA to protein in a two-step process involving transcription and translation. In the biological stage, DNA replication was central to the binary fission of the first cell, orchestrated by the duplication of genomes and then the division of the parent cell into two identical daughter cells. With the onset of binary fission, the population of primitive cells grew rapidly in the hydrothermal vent environment, undergoing Darwinian evolution and diversification by mutation. The habitat of the earliest fossil record (≥ 3.5 Ga) from the Archean sedimentary rocks of Canada, Greenland, Australia, South Africa, and India offers a new window on the early radiation of microbial life. The development of anoxygenic and then oxygenic photosynthesis from early hyperthermophiles would have allowed life to escape the hydrothermal setting to the mesophilic global ocean.