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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) -
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. -
Enforcement Is Central to the Evolution of Cooperation
REVIEW ARTICLE https://doi.org/10.1038/s41559-019-0907-1 Enforcement is central to the evolution of cooperation J. Arvid Ågren1,2,6, Nicholas G. Davies 3,6 and Kevin R. Foster 4,5* Cooperation occurs at all levels of life, from genomes, complex cells and multicellular organisms to societies and mutualisms between species. A major question for evolutionary biology is what these diverse systems have in common. Here, we review the full breadth of cooperative systems and find that they frequently rely on enforcement mechanisms that suppress selfish behaviour. We discuss many examples, including the suppression of transposable elements, uniparental inheritance of mito- chondria and plastids, anti-cancer mechanisms, reciprocation and punishment in humans and other vertebrates, policing in eusocial insects and partner choice in mutualisms between species. To address a lack of accompanying theory, we develop a series of evolutionary models that show that the enforcement of cooperation is widely predicted. We argue that enforcement is an underappreciated, and often critical, ingredient for cooperation across all scales of biological organization. he evolution of cooperation is central to all living systems. A major open question, then, is what, if anything, unites the Evolutionary history can be defined by a series of major tran- evolution of cooperative systems? Here, we review cooperative evo- Tsitions (Box 1) in which replicating units came together, lost lution across all levels of biological organization, which reveals a their independence and formed new levels of biological organiza- growing amount of evidence for the importance of enforcement. tion1–4. As a consequence, life is organized in a hierarchy of coop- By enforcement, we mean an action that evolves, at least in part, to eration: genes work together in genomes, genomes in cells, cells in reduce selfish behaviour within a cooperative alliance (see Box 2 for multicellular organisms and multicellular organisms in eusocial the formal definition). -
Latin Derivatives Dictionary
Dedication: 3/15/05 I dedicate this collection to my friends Orville and Evelyn Brynelson and my parents George and Marion Greenwald. I especially thank James Steckel, Barbara Zbikowski, Gustavo Betancourt, and Joshua Ellis, colleagues and computer experts extraordinaire, for their invaluable assistance. Kathy Hart, MUHS librarian, was most helpful in suggesting sources. I further thank Gaylan DuBose, Ed Long, Hugh Himwich, Susan Schearer, Gardy Warren, and Kaye Warren for their encouragement and advice. My former students and now Classics professors Daniel Curley and Anthony Hollingsworth also deserve mention for their advice, assistance, and friendship. My student Michael Kocorowski encouraged and provoked me into beginning this dictionary. Certamen players Michael Fleisch, James Ruel, Jeff Tudor, and Ryan Thom were inspirations. Sue Smith provided advice. James Radtke, James Beaudoin, Richard Hallberg, Sylvester Kreilein, and James Wilkinson assisted with words from modern foreign languages. Without the advice of these and many others this dictionary could not have been compiled. Lastly I thank all my colleagues and students at Marquette University High School who have made my teaching career a joy. Basic sources: American College Dictionary (ACD) American Heritage Dictionary of the English Language (AHD) Oxford Dictionary of English Etymology (ODEE) Oxford English Dictionary (OCD) Webster’s International Dictionary (eds. 2, 3) (W2, W3) Liddell and Scott (LS) Lewis and Short (LS) Oxford Latin Dictionary (OLD) Schaffer: Greek Derivative Dictionary, Latin Derivative Dictionary In addition many other sources were consulted; numerous etymology texts and readers were helpful. Zeno’s Word Frequency guide assisted in determining the relative importance of words. However, all judgments (and errors) are finally mine. -
Sustainable Growth and Synchronization in Protocell Models
life Article Sustainable Growth and Synchronization in Protocell Models Roberto Serra 1,2,3 and Marco Villani 1,2,* 1 Department of Physics, Informatics and Mathematics, Modena and Reggio Emilia University, Via Campi 213/A, 41125 Modena, Italy 2 European Centre for Living Technology, Ca’ Bottacin, Dorsoduro 3911, Calle Crosera, 30123 Venice, Italy 3 Institute for Advanced Study, University of Amsterdam, Oude Turfmarkt 147, 1012 GC Amsterdam, The Netherlands * Correspondence: [email protected] Received: 19 July 2019; Accepted: 14 August 2019; Published: 21 August 2019 Abstract: The growth of a population of protocells requires that the two key processes of replication of the protogenetic material and reproduction of the whole protocell take place at the same rate. While in many ODE-based models such synchronization spontaneously develops, this does not happen in the important case of quadratic growth terms. Here we show that spontaneous synchronization can be recovered (i) by requiring that the transmembrane diffusion of precursors takes place at a finite rate, or (ii) by introducing a finite lifetime of the molecular complexes. We then consider reaction networks that grow by the addition of newly synthesized chemicals in a binary polymer model, and analyze their behaviors in growing and dividing protocells, thereby confirming the importance of (i) and (ii) for synchronization. We describe some interesting phenomena (like long-term oscillations of duplication times) and show that the presence of food-generated autocatalytic cycles is not sufficient to guarantee synchronization: in the case of cycles with a complex structure, it is often observed that only some subcycles survive and synchronize, while others die out. -
Rose's Homeodynamic Perspective Is Not an Alternative to Neo-Darwinism
Andrew J. Wells Rose's homeodynamic perspective is not an alternative to Neo-Darwinism Article (Published version) (Refereed) Original citation: Wells, Andrew J. (1999) Rose's homeodynamic perspective is not an alternative to Neo- Darwinism. Behavioral and brain sciences, 22 (5). pp. 911-912. ISSN 0140-525X DOI:10.1017/S0140525X9951220X © 1999 Cambridge University Press This version available at: http://eprints.lse.ac.uk/12103/ Available in LSE Research Online: August 2012 LSE has developed LSE Research Online so that users may access research output of the School. Copyright © and Moral Rights for the papers on this site are retained by the individual authors and/or other copyright owners. Users may download and/or print one copy of any article(s) in LSE Research Online to facilitate their private study or for non-commercial research. You may not engage in further distribution of the material or use it for any profit-making activities or any commercial gain. You may freely distribute the URL (http://eprints.lse.ac.uk) of the LSE Research Online website. BEHAVIORAL AND BRAIN SCIENCES (1999) 22, 871–921 Printed in the United States of America Précis of Lifelines: Biology, freedom, determinism1 Steven Rose Biology Department, Brain and Behaviour Research Group, Open University, Milton Keynes, MK7 6AA, United Kingdom. [email protected] Abstract: There are many ways of describing and explaining the properties of living systems; causal, functional, and reductive accounts are necessary but no one account has primacy. The history of biology as a discipline has given excessive authority to reductionism, which collapses higher level accounts, such as social or behavioural ones, into molecular ones. -
Protocells and RNA Self-Replication
Downloaded from http://cshperspectives.cshlp.org/ at MASS GENERAL HOSPITAL on September 8, 2018 - Published by Cold Spring Harbor Laboratory Press Protocells and RNA Self-Replication Gerald F. Joyce1 and Jack W. Szostak2 1The Salk Institute for Biological Studies, La Jolla, California 92037 2Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114 Correspondence: [email protected]; [email protected] SUMMARY The general notion of an “RNA world” is that, in the early development of life on the Earth, genetic continuity was assured by the replication of RNA, and RNA molecules were the chief agents of catalytic function. Assuming that all of the components of RNA were available in some prebiotic locale, these components could have assembled into activated nucleotides that condensed to form RNA polymers, setting the stage for the chemical replication of polynucle- otides through RNA-templated RNA polymerization. If a sufficient diversity of RNAs could be copied with reasonable rate and fidelity, then Darwinian evolution would begin with RNAs that facilitated their own reproduction enjoying a selective advantage. The concept of a “pro- tocell” refers to a compartment where replication of the primitive genetic material took place and where primitive catalysts gave rise to products that accumulated locally for the benefit of the replicating cellular entity. Replication of both the protocell and its encapsulated genetic material would have enabled natural selection to operate based on the differential fitness of competing cellular entities, ultimately giving rise to modern cellular life. Outline 1 Introduction 5 RNA-catalyzed replication systems 2 Compartmentalized systems 6 Compartmented genetics 3 Nature of the first genetic material 7 Summary 4 Chemical RNA replication systems References Editors: Thomas R. -
Origin of Species Before Origin of Life: the Role of Speciation in Chemical Evolution
life Review Origin of Species before Origin of Life: The Role of Speciation in Chemical Evolution Tony Z. Jia 1,2,* , Melina Caudan 1 and Irena Mamajanov 1,* 1 Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan; [email protected] 2 Blue Marble Space Institute of Science, 1001 4th Ave., Suite 3201, Seattle, WA 98154, USA * Correspondence: [email protected] (T.Z.J.); [email protected] (I.M.) Abstract: Speciation, an evolutionary process by which new species form, is ultimately responsible for the incredible biodiversity that we observe on Earth every day. Such biodiversity is one of the critical features which contributes to the survivability of biospheres and modern life. While speciation and biodiversity have been amply studied in organismic evolution and modern life, it has not yet been applied to a great extent to understanding the evolutionary dynamics of primitive life. In particular, one unanswered question is at what point in the history of life did speciation as a phenomenon emerge in the first place. Here, we discuss the mechanisms by which speciation could have occurred before the origins of life in the context of chemical evolution. Specifically, we discuss that primitive compartments formed before the emergence of the last universal common ancestor (LUCA) could have provided a mechanism by which primitive chemical systems underwent speciation. In particular, we introduce a variety of primitive compartment structures, and associated functions, that may have plausibly been present on early Earth, followed by examples of both discriminate and indiscriminate speciation affected by primitive modes of compartmentalization. -
SCB255 Course Title: Cell Biology Department
CELL BIOLOGY Course ID: SCB255 Course Title: Cell Biology Department: Natural Sciences Discipline: SCB-Biology Course Credits: 4 credits 6 hours (3 lecture, 3 laboratory) Course Coordinator: Dr. Thomas M. Onorato ([email protected]) Required Textbook: Essential Cell Biology, 4th Edition, Bruce Alberts et al., 2013 (ISBN 978-0-8153-4525-1), Publisher: Garland Science Course Description: This is a one-semester laboratory-based course stressing essential aspects of cell biology. Cell structure and function will be introduced. Topics to be covered include, but are not limited to, membrane transport, protein sorting, vesicular trafficking, cytoskeletal components, how cells read the genome, signal transduction, cancer, apoptosis, and stem cells. Students will conduct authentic undergraduate research projects involving cell culture. Prerequisite: SCB252, ENG102, SCB202, SCC202 Grading: Midterm & Final exams (15% ea) 30% 4 assignments @ 5% each 20% Research manuscript 20% Research project design 10% ePortfolio 10% 1 Literature presentation 10% 100% ARTIFACT ASSESSMENT This class will be depositing student work for this semester. Students will be depositing assignments for: 1) Inquiry and Problem Solving Written ability 2) Global Learning competency Oral Communication ability 3) Integrative Learning Digital ability For a tutorial on how to deposit student work, go to: http://eportfolio.lagcc.cuny.edu/support/tutorials.htm and find the section called, “Assessment for Students.” Click on the adobe flash button for “Depositing Assessment Artifact in Digication Instructions for Students.” You will see a brief video on how to deposit. PERFORMANCE OBJECTIVES: 1. Interpret the concepts of basic cell structure and function. 2. Describe the transcriptional, post-transcriptional and post-translational control of gene expression. -
Droplets: Unconventional Protocell Model with Life-Like Dynamics and Room to Grow
Life 2014, 4, 1038-1049; doi:10.3390/life4041038 OPEN ACCESS life ISSN 2075-1729 www.mdpi.com/journal/life Review Droplets: Unconventional Protocell Model with Life-Like Dynamics and Room to Grow Martin M Hanczyc Centre for Integrative Biology (CIBIO), University of Trento, Via Sommarive, 9 I-38123 Povo (TN), Italy; E-Mail: [email protected] External Editors: Fabio Mavelli and Pasquale Stano Received: 31 October 2014; in revised form: 8 December 2014 / Accepted: 11 December 2014 / Published: 17 December 2014 Abstract: Over the past few decades, several protocell models have been developed that mimic certain essential characteristics of living cells. These protocells tend to be highly reductionist simplifications of living cells with prominent bilayer membrane boundaries, encapsulated metabolisms and/or encapsulated biologically-derived polymers as potential sources of information coding. In parallel with this conventional work, a novel protocell model based on droplets is also being developed. Such water-in-oil and oil-in-water droplet systems can possess chemical and biochemical transformations and biomolecule production, self-movement, self-division, individuality, group dynamics, and perhaps the fundamentals of intelligent systems and evolution. Given the diverse functionality possible with droplets as mimics of living cells, this system has the potential to be the first true embodiment of artificial life that is an orthologous departure from the one familiar type of biological life. This paper will synthesize the recent activity to develop droplets as protocell models. Keywords: artificial cells; droplets; convection; emergence of life; fluid dynamics; minimal cells; origin of life; protocells 1. Droplets The droplet consists simply of a liquid compartment that is highly insoluble in another liquid. -
Reciprocal Linkage Between Self-Organizing Processes Is Sufficient for Self-Reproduction and Evolvability
Reciprocal Linkage between Self-organizing Processes is Sufficient for Self-reproduction and Evolvability Terrence W. Deacon Abstract Department of Anthropology and Helen Wills Neuroscience Institute A simple molecular system (“autocell”) is described consisting University of California, Berkeley, CA, USA of the reciprocal linkage between an autocatalytic cycle and [email protected] a self-assembling encapsulation process where the molecular constituents for the capsule are products of the autocatalysis. In a molecular environment sufficiently rich in the substrates, capsule growth will also occur with high predictability. Growth to closure will be most probable in the vicinity of the most pro- lific autocatalysis and will thus tend to spontaneously enclose supportive catalysts within the capsule interior. If subsequently disrupted in the presence of new substrates, the released com- ponents will initiate production of additional catalytic and cap- sule components that will spontaneously re-assemble into one or more autocell replicas, thereby reconstituting and some- times reproducing the original. In a diverse molecular envi- ronment, cycles of disruption and enclosure will cause auto- cells to incidentally encapsulate other molecules as well as reactive substrates. To the extent that any captured molecule can be incorporated into the autocatalytic process by virtue of structural degeneracy of the catalytic binding sites, the al- tered autocell will incorporate the new type of component into subsequent replications. Such altered autocells will be progenitors of “lineages” with variant characteristics that will differentially propagate with respect to the availability of com- monly required substrates. Autocells are susceptible to a lim- ited form of evolution, capable of leading to more efficient, more environmentally fitted, and more complex forms.