Directionality Theory and the Entropic Principle of Natural Selection
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Framing Major Prebiotic Transitions As Stages of Protocell Development: Three Challenges for Origins-Of-Life Research
Framing major prebiotic transitions as stages of protocell development: three challenges for origins-of-life research Ben Shirt-Ediss1, Sara Murillo-Sánchez2,3 and Kepa Ruiz-Mirazo*2,3 Commentary Open Access Address: Beilstein J. Org. Chem. 2017, 13, 1388–1395. 1Interdisciplinary Computing and Complex BioSystems Group, doi:10.3762/bjoc.13.135 University of Newcastle, UK, 2Dept. Logic and Philosophy of Science, University of the Basque Country, Spain and 3Biofisika Institute Received: 16 February 2017 (CSIC, UPV-EHU), Spain Accepted: 27 June 2017 Published: 13 July 2017 Email: Kepa Ruiz-Mirazo* - [email protected] This article is part of the Thematic Series "From prebiotic chemistry to molecular evolution". * Corresponding author Guest Editor: L. Cronin Keywords: functional integration; origins of life; prebiotic evolution; protocells © 2017 Shirt-Ediss et al.; licensee Beilstein-Institut. License and terms: see end of document. Abstract Conceiving the process of biogenesis as the evolutionary development of highly dynamic and integrated protocell populations provides the most appropriate framework to address the difficult problem of how prebiotic chemistry bridged the gap to full-fledged living organisms on the early Earth. In this contribution we briefly discuss the implications of taking dynamic, functionally inte- grated protocell systems (rather than complex reaction networks in bulk solution, sets of artificially evolvable replicating molecules, or even these same replicating molecules encapsulated in passive compartments) -
Chapter 9. NATURAL SELECTION and BIOLOGICAL EVOLUTION
Chapter 9. NATURAL SELECTION AND BIOLOGICAL EVOLUTION Which beginning of time [the Creation] according to our Chronologie, fell upon the entrance of the night preced- ing the twenty third day of Octob. in the year of the Julian Calendar, 710 [i.e. B.C. 4004]. Archbishop James Ussher (1581—1656) The Annals of the World1 (1658:1) “How stupid not to have thought of that!” Thomas Huxley (1825-1895), about Darwin’s theory of Evolution by Nat- ural Selection. I. Introduction A. Classical Discoveries of Biology From the mid 18th Century to the early part of the 20th, a large fraction of biologists’ efforts went into two massive collective discoveries, the discovery of biotic diversity, and the discovery of evolution. Over the period from 1750 to 1950 the careful descriptive analyses of Swedish biol- ogist Karl von Linné and his followers showed there to be on the order of 10 million or so different types of living organisms. The differences in biotas in different parts of the world came to be appreciated, the amazing diversity of the tropics was documented, and previ- ously unimagined major groups of organisms were discovered, including microorganisms and the biota of odd habitats like the oceanic plankton. The sometimes bizarre and always impressive adaptation of organisms to their habitats and ways of life greatly impressed the early scientific naturalists, who argued that it proved the existence of an All Seeing Design- er. Similarly, paleontologists described a huge variety of fossil plants and animals. The succession of forms, and the presence of many detailed structural similarities between liv- ing and extinct forms, as well as structural parallels between living forms, strongly suggest- ed that living and ancient forms of life were connected by branching lines of descent. -
Uniting Micro- with Macroevolution Into an Extended Synthesis: Reintegrating Life’S Natural History Into Evolution Studies
Uniting Micro- with Macroevolution into an Extended Synthesis: Reintegrating Life’s Natural History into Evolution Studies Nathalie Gontier Abstract The Modern Synthesis explains the evolution of life at a mesolevel by identifying phenotype–environmental interactions as the locus of evolution and by identifying natural selection as the means by which evolution occurs. Both micro- and macroevolutionary schools of thought are post-synthetic attempts to evolution- ize phenomena above and below organisms that have traditionally been conceived as non-living. Microevolutionary thought associates with the study of how genetic selection explains higher-order phenomena such as speciation and extinction, while macroevolutionary research fields understand species and higher taxa as biological individuals and they attribute evolutionary causation to biotic and abiotic factors that transcend genetic selection. The microreductionist and macroholistic research schools are characterized as two distinct epistemic cultures where the former favor mechanical explanations, while the latter favor historical explanations of the evolu- tionary process by identifying recurring patterns and trends in the evolution of life. I demonstrate that both cultures endorse radically different notions on time and explain how both perspectives can be unified by endorsing epistemic pluralism. Keywords Microevolution · Macroevolution · Origin of life · Evolutionary biology · Sociocultural evolution · Natural history · Organicism · Biorealities · Units, levels and mechanisms of evolution · Major transitions · Hierarchy theory But how … shall we describe a process which nobody has seen performed, and of which no written history gives any account? This is only to be investigated, first, in examining the nature of those solid bodies, the history of which we want to know; and 2dly, in exam- ining the natural operations of the globe, in order to see if there now actually exist such operations, as, from the nature of the solid bodies, appear to have been necessary to their formation. -
Species Extinctions
http://www.iucn.org/about/union/commissions/wcpa/?7695/Multiple-ocean-stresses- threaten-globally-significant-marine-extinction Multiple ocean stresses threaten “globally significant” marine extinction 20 June 2011 | News story An international panel of experts warns in a report released today that marine species are at risk of entering a phase of extinction unprecedented in human history. The preliminary report arises from a ‘State of the Oceans’ workshop co-hosted by IUCN in April, the first ever to consider the cumulative impact of all pressures on the oceans. Considering the latest research across all areas of marine science, the workshop examined the combined effects of pollution, acidification, ocean warming, over-fishing and hypoxia (deoxygenation). The scientific panel concluded that the combination of stresses on the ocean is creating the conditions associated with every previous major extinction of species in Earth’s history. And the speed and rate of degeneration in the ocean is far greater than anyone has predicted. The panel concluded that many of the negative impacts previously identified are greater than the worst predictions. As a result, although difficult to assess, the first steps to globally significant extinction may have begun with a rise in the extinction threat to marine species such as reef- forming corals. “The world’s leading experts on oceans are surprised by the rate and magnitude of changes we are seeing,” says Dan Laffoley, Marine Chair of IUCN’s World Commission on Protected Areas, Senior Advisor on Marine Science and Conservation for IUCN and co-author of the report. “The challenges for the future of the ocean are vast, but unlike previous generations, we know what now needs to happen. -
Effect of Irradiation of the PEM of 1.531211SMJ29 Jeewanu with Clinical Mercury Lamp and Sunlight on the Morphological Features of the Silicon Molybdenum Jeewanu
International Journal of Engineering Research and General Science Volume 4, Issue 4, July-August, 2016 ISSN 2091-2730 Effect of Irradiation of the PEM of 1.531211SMJ29 Jeewanu with Clinical Mercury Lamp and Sunlight on the Morphological Features of the Silicon Molybdenum Jeewanu Deepa Srivastava Department of Chemistry, S.S.Khanna Girls‘ Degree College, Constituent College of Allahabad University, Allahabad, Uttar Pradesh, India E- Mail – [email protected] Abstract— Sterilized aqueous mixture of ammonium molybdate, diammonium hydrogen phosphate, mineral solution and formaldehyde on exposure to sunlight results in the formation of self-sustaining coacervates which were coined as Jeewanu, the autopoetic eukaryote by Bahadur and Ranganayaki. Jeewanu have been analyzed to contain a number of compounds of biological interest. The presence of various enzyme like activities viz., phosphatase, ATP-ase, esterase, nitrogenase have been also been detected in Jeewanu mixture. Gáinti (2003) discussed that Jeewanu possesses a promising configuration similar to protocell-like model. Keywords— Autopoetic, eukaryote, Jeewanu, PEM, sunlight, mercury lamp, morphology, 1.531211SMJ29 INTRODUCTION Sterilized aqueous mixture of ammonium molybdate, diammonium hydrogen phosphate, mineral solution and formaldehyde on exposure to sunlight results in the formation of self-sustaining coacervates which were coined as Jeewanu, the autopoetic eukaryote by Bahadur, K and Ranganayaki, S. in 1970. [1] The photochemical, formation of protocell-like microstructures ―Jeewanu‖ in a laboratory simulated prebiotic atmosphere capable of showing multiplication by budding, growth from within by actual synthesis of material and various metabolic activities has been reported by Bahadur et al. [1, 2, 3, 4, 5, 7, 8] Jeewanu have been analyzed to contain a number of compounds of biological interest viz. -
Constructing Protocells: a Second Origin of Life
04_SteenRASMUSSEN.qxd:Maqueta.qxd 4/6/12 11:45 Página 585 Session I: The Physical Mind CONSTRUCTING PROTOCELLS: A SECOND ORIGIN OF LIFE STEEN RASMUSSEN Center for Fundamental Living Technology (FLinT) Santa Fe Institute, New Mexico USA ANDERS ALBERTSEN, PERNILLE LYKKE PEDERSEN, CARSTEN SVANEBORG Center for Fundamental Living Technology (FLinT) ABSTRACT: What is life? How does nonliving materials become alive? How did the first living cells emerge on Earth? How can artificial living processes be useful for technology? These are the kinds of questions we seek to address by assembling minimal living systems from scratch. INTRODUCTION To create living materials from nonliving materials, we first need to understand what life is. Today life is believed to be a physical process, where the properties of life emerge from the dynamics of material interactions. This has not always been the assumption, as living matter at least since the origin of Hindu medicine some 5000 years ago, was believed to have a metaphysical vital force. Von Neumann, the inventor of the modern computer, realized that if life is a physical process it should be possible to implement life in other media than biochemistry. In the 1950s, he was one of the first to propose the possibilities of implementing living processes in computers and robots. This perspective, while being controversial, is gaining momentum in many scientific communities. There is not a generally agreed upon definition of life within the scientific community, as there is a grey zone of interesting processes between nonliving and living matter. Our work on assembling minimal physicochemical life is based on three criteria, which most biological life forms satisfy. -
Reproduction of a Protocell by Replication of Minority Molecule in Catalytic Reaction Network
APS/123-QED Reproduction of a Protocell by Replication of Minority Molecule in Catalytic Reaction Network Atsushi Kamimura1 and Kunihiko Kaneko2, 3 1Department of Applied Physics, Graduate School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8656, Japan. 2Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1, Komaba, Meguro-ku, Tokyo 153-8902, Japan 3Complex Systems Biology Project, ERATO, JST, Tokyo, Japan. (Dated: October 31, 2018) Abstract For understanding the origin of life, it is essential to explain the development of a compartmen- talized structure, which undergoes growth and division, from a set of chemical reactions. In this study, a hypercycle with two chemicals that mutually catalyze each other is considered in order to show that the reproduction of a protocell with a growth-division process naturally occurs when the replication speed of one chemical is considerably slower than that of the other chemical. It is observed that the protocell divides after a minority molecule is replicated at a slow synthesis rate, and thus, a synchrony between the reproduction of a cell and molecule replication is achieved. The robustness of such protocells against the invasion of parasitic molecules is also demonstrated. arXiv:1005.1142v1 [q-bio.CB] 7 May 2010 PACS numbers: 87.17.-d, 05.40.-a, 82.39.-k 1 Filling a gap between just a set of catalytic reactions and a reproducing cell is a difficult problem; however, it is essential to fully understand this relationship to unveil the origin of life, to establish a theory for a living state, and to experimentally synthesize protocells[1]. -
Simple Stochastic Populations in Habi- Tats with Bounded, and Varying Carry- Ing Capacities
Simple Stochastic Populations in Habi- tats with Bounded, and Varying Carry- ing Capacities Master’s thesis in Complex Adaptive Systems EDWARD KORVEH Department of Mathematical Sciences CHALMERS UNIVERSITY OF TECHNOLOGY Gothenburg, Sweden 2016 Master’s thesis 2016:NN Simple Stochastic Populations in Habitats with Bounded, and Varying Carrying Capacities EDWARD KORVEH Department of Mathematical Sciences Division of Mathematical Statistics Chalmers University of Technology Gothenburg, Sweden 2016 Simple Stochastic Populations in Habitats with Bounded, and Varying Carrying Capacities EDWARD KORVEH © EDWARD KORVEH, 2016. Supervisor: Peter Jagers, Department of Mathematical Sciences Examiner: Peter Jagers, Department of Mathematical Sciences Master’s Thesis 2016:NN Department of Mathematical Sciences Division of Mathematical Statistics Chalmers University of Technology SE-412 96 Gothenburg Gothenburg, Sweden 2016 iv Simple Stochastic Populations in Habitats with Bounded, and Varying Carrying Capacities EDWARD KORVEH Department of Mathematical Sciences Chalmers University of Technology Abstract A population consisting of one single type of individuals where reproduction is sea- sonal, and by means of asexual binary-splitting with a probability, which depends on the carrying capacity of the habitat, K and the present population is considered. Current models for such binary-splitting populations do not explicitly capture the concepts of early and late extinctions. A new parameter v, called the ‘scaling pa- rameter’ is introduced to scale down the splitting probabilities in the first season, and also in subsequent generations in order to properly observe and record early and late extinctions. The modified model is used to estimate the probabilities of early and late extinctions, and the expected time to extinction in two main cases. -
The Sixth Great Extinction Donations Events "Soon a Millennium Will End
The Rewilding Institute, Dave Foreman, continental conservation Home | Contact | The EcoWild Program | Around the Campfire About Us Fellows The Pleistocene-Holocene Event: Mission Vision The Sixth Great Extinction Donations Events "Soon a millennium will end. With it will pass four billion years of News evolutionary exuberance. Yes, some species will survive, particularly the smaller, tenacious ones living in places far too dry and cold for us to farm or graze. Yet we Resources must face the fact that the Cenozoic, the Age of Mammals which has been in retreat since the catastrophic extinctions of the late Pleistocene is over, and that the Anthropozoic or Catastrophozoic has begun." --Michael Soulè (1996) [Extinction is the gravest conservation problem of our era. Indeed, it is the gravest problem humans face. The following discussion is adapted from Chapters 1, 2, and 4 of Dave Foreman’s Rewilding North America.] Click Here For Full PDF Report... or read report below... Many of our reports are in Adobe Acrobat PDF Format. If you don't already have one, the free Acrobat Reader can be downloaded by clicking this link. The Crisis The most important—and gloomy—scientific discovery of the twentieth century was the extinction crisis. During the 1970s, field biologists grew more and more worried by population drops in thousands of species and by the loss of ecosystems of all kinds around the world. Tropical rainforests were falling to saw and torch. Wetlands were being drained for agriculture. Coral reefs were dying from god knows what. Ocean fish stocks were crashing. Elephants, rhinos, gorillas, tigers, polar bears, and other “charismatic megafauna” were being slaughtered. -
According to Science Ramy Brustein Ben-Gurion University of the Negev
The Creation of the World – According to Science Ramy Brustein Ben-Gurion University of the Negev How was the world created? People have asked this ever since they could ask anything, and answers have come from all sides: from religion, tradition, philosophy, mysticism….and science. While this does not seem like a problem amenable to scientific measurement, it has led scientists to come up with fascinating ideas and observations: the Big Bang, the concept of inflation, the fact that most of the world is made up of dark matter and dark energy which we cannot perceive, and more. Of course scientists cannot claim to know the definitive truth. But we can approach the question from a scientific viewpoint and see what we find out. How do we do that? First, we look to the data. Thanks to modern technology, we have much more information than did people of previous ages who asked the same question. Then we can use scientific methods and techniques to analyze the data, organize them in a coherent way and try and extract an answer. This process and its main findings will be described in the lecture. The Ghosts in the (Primitive) Soup: A Review of Some of the Debates that Shaped Early Discussions on the Origin and Nature of Life Antonio Lazcano Universidad Nacional Autónoma de México The heterotrophic origin of life proposed by Oparin and Haldane in the 1920’s was part of a Darwinian framework that assumed that living organisms were the historical outcome of a gradual transformation of lifeless matter. This idea was strongly opposed by the geneticist H. -
Evolution, Development, and the Units of Selection (Epigenesis/Modern Synthesis/Preformation/Somatic Embryogenesis/Weismann's Doctrine) LEO W
Proc. Nat. Acad. Sci. USA Vol. 80, pp. 1387-1391, March 1983 Evolution Evolution, development, and the units of selection (epigenesis/Modern Synthesis/preformation/somatic embryogenesis/Weismann's doctrine) LEO W. Buss Department of Biology and Peabody Museum of Natural History, Yale University, New Haven, Connecticut 06511 Communicated by G, Evelyn Hutchinson, December 17, 1982 ABSTRACT The "Modern Synthesis" forms the foundation of those working with the comparative embryology of vertebrates, current evolutionary theory. It is based on variation among indi- saw strong evidence for Weismann's scheme in the sequestering viduals within populations. Variations within individuals are be- of germ cells during early embryology. Finally, several inves- lieved to hold no phylogenetic significance because such variation tigators studying wound-healing had clearly illustrated that many cannot be transmitted to the germ line (i.e., Weismann's doctrine). somatic cells were, in fact, incapable of regeneration. Weismann's doctrine, however, does not apply to protists, fungi, Support for Weismann's doctrine was by no means universal. or plants and is an entirely unsupported assumption for 19 phyla Botanists were Weismann's earliest critics (5). Debate over the of animals. This fact requires that the Modern Synthesis be reex- issue was central in the development of the continuing rift be- amined and modified. tween botanists and zoologists despite the commonality of their interests (G. E. Hutchinson, personal communication). Al- The Darwinian notion of evolution as a process directed by se- though Weismann's doctrine was the subject of two very critical lection acting upon heritable variation has not been challenged reviews in the 20th century (6, 7), these criticisms fell on deaf seriously since Darwin first articulated it. -
Assessing the Record and Causes of Late Triassic Extinctions
Earth-Science Reviews 65 (2004) 103–139 www.elsevier.com/locate/earscirev Assessing the record and causes of Late Triassic extinctions L.H. Tannera,*, S.G. Lucasb, M.G. Chapmanc a Departments of Geography and Geoscience, Bloomsburg University, Bloomsburg, PA 17815, USA b New Mexico Museum of Natural History, 1801 Mountain Rd. N.W., Albuquerque, NM 87104, USA c Astrogeology Team, U.S. Geological Survey, 2255 N. Gemini Rd., Flagstaff, AZ 86001, USA Abstract Accelerated biotic turnover during the Late Triassic has led to the perception of an end-Triassic mass extinction event, now regarded as one of the ‘‘big five’’ extinctions. Close examination of the fossil record reveals that many groups thought to be affected severely by this event, such as ammonoids, bivalves and conodonts, instead were in decline throughout the Late Triassic, and that other groups were relatively unaffected or subject to only regional effects. Explanations for the biotic turnover have included both gradualistic and catastrophic mechanisms. Regression during the Rhaetian, with consequent habitat loss, is compatible with the disappearance of some marine faunal groups, but may be regional, not global in scale, and cannot explain apparent synchronous decline in the terrestrial realm. Gradual, widespread aridification of the Pangaean supercontinent could explain a decline in terrestrial diversity during the Late Triassic. Although evidence for an impact precisely at the boundary is lacking, the presence of impact structures with Late Triassic ages suggests the possibility of bolide impact-induced environmental degradation prior to the end-Triassic. Widespread eruptions of flood basalts of the Central Atlantic Magmatic Province (CAMP) were synchronous with or slightly postdate the system boundary; emissions of CO2 and SO2 during these eruptions were substantial, but the contradictory evidence for the environmental effects of outgassing of these lavas remains to be resolved.