Protocells {ReadingNotes}

Protocells: Bridging Nonliving and Living Matter - ISBN 0262182688 - MIT Press 2008

Skimming

• first pass with titles and conclusions
  • three functional components (Figure I.1 in the Introduction
    courtesy of the FLinT, Center for Fundamental Living Technology, University of Southern Denmark)
    • metabolism
    • container
    • genes
  • virtual models
    • software
      • Virtual Cell NRCAM
      • Programmable Artificial Cell Evolution
      • see the long list (p?)
    • cognitive framework
      • chemoton
      • Lattice artificial chemistry
      • Lattice molecular automaton
      • see the ending glossary (p?)
      • (not in the book) Conductance-based models seem to be pretty related too
  • fractal pattern of ontogenic growth
    • 8 - Constructive Approach to Protocells: Theory and Experiments
      • 8.3 Theoretical Issue 2: Origin of Recursive Production and Evolvability
  • seems to have nearly no occurance of "cognition" but plenty of "recognition"
    • probably highlighting the importance of the membrane
      • still key to Stewart's life=cognition (never mentioned in the book)
  • enaction by Varela/Maturana
    • chapters referencing Maturana, H., & Varela, F. (1980). Autopoiesis and cognition: The realization of the living
      • 3 - Semisynthetic Minimal Cells
      • 4 - A Roadmap to Protocells
      • 9 - Origin of Life and Lattice Artificial Chemistry
      • 12 - Evolutionary Microfluidic Complementation Toward Artificial Cells
      • 22 - Ganti’s Chemoton Model and Life Criteria
  • 20 - Core Metabolism as a Self-Organized System
    • "Metabolism of protocells should be based on pathways with the lowest thresholds to autocatalysis."
    • "We suggest that the order of life should be understood as a statistical phenomenon, from the smallest to the largest structures, and from the earliest chemical stages to the persistence of modern forms."
  • 21 - Energetics, Energy Flow, and Scaling in Life
    • 21.4 - Energy and Information (p469)
  • 24 - Nonlinear Chemical Dynamics and the Origin of Life
    • Conclusion, 2, "The Darwinian evolution with its exponential growth occurs once one has the capacity for self-catalysis, or perhaps more accurately, self-driven reproduction, with evolution occurring as a result of occasional errors in the self-reproduction process, with the defective product still having the ability to self-reproduce. Competition for resources coupled with the environment itself will, of course, provide the subsequent selection." (p560)

Overall questions and remarks

• life a self-sustaining process relying on sub-processes and mainly homeostasis

See also

• my notes on The Things We Do: Using the Lessons of Bernard and Darwin to Understand the What, How, and Why of Our Behavior]] by Gary Cziko
• The EvoGrid: The Evolution Technology Grid by Bruce Damer et al.
• Did evolution come before life? by Bob Holmes, New Scientist 2008
• Shapes and Self-Movement in Protocell Systems by Keisuke Suzuki and Takashi Ikegami, Artificial Life Winter 2009
• Evolvable Self-Reproducing Cells in a Two-Dimensional Artificial Chemistry by Tim J. Hutton, Artificial Life Winter 2007
• Was our oldest ancestor a proton-powered rock? by Nick Lane, New Scientist October 2009
  • How life evolved: 10 steps to the first cells by Nick Lane and Michael Le Page, New Scientist October 2009
  • Chemiosmosis "the diffusion of ions across a selectively-permeable membrane." according to Wikipedia
  • Electron Transport Chain Animation Overview (Chemiosmosis), DaggerBiology 2008
• A l’origine de la vie, La marche des sciences, France Culture December 2009
• Alife XII 2010 at the Center for Fundamental Living Technology (FLinT) at University of Southern Denmark (SDU)
• the emerging field of systems chemistry
  • Journal of Systems Chemistry dealing with several topics including
    • catalytic and autocatalytic systems
    • self-replicating and self-reproducing chemical systems
  • Instant insight: Systems chemistry Chemical Science by RSC Publishing 2007
• Venter’s Successes in Creating Synthetic Life by Aaron Saenz, Singularity Hub February 2010
• Pine Group Web Pages Department of Physics and Center for Soft Matter Research at New York University
  • self-assembly, both to understand how nature employs it to form complex and useful structures, and to develop methods to manipulate it to make interesting new materials.
  • Spherical Life: Schemes for Colloidal Self-Replication by David Pine, ENS February 2010
    • cf the earlier conference watched a year ealier, February 2009, DNA Self-assembly and Computer System Fabrication by Chris Dwyer from Duke University, ResearchChannel, 2007
• Researchers start up cell with synthetic genome Nature News May 2010
  • JCVI: Research First Self-Replicating Synthetic Bacterial Cell funded by Synthetic Genomics, Inc.
  • Synthetic biology: And man made life The Economist May 2010
• Earliest sense is for monastic rooms, then prison rooms (1722). Used in 14c., figuratively, of brain "compartments;" used in biology 17c. of various cavities Cell according to the Online Etymology Dictionary
  • Wikipedia:Cell (biology)#History
  • discovered thanks to The Story of Science: Power, Proof and Passion : What Is the Secret of Life?, BBC May 2010
• Protocells by Rachel Armstrong
• Wikipedia:Hypercycle (chemistry) by Wikipedia:Manfred Eigen Wikipedia:Peter Schuster
• Wikipedia:Quasispecies model
• The Origins of Life edited By David Deamer and Jack W. Szostak, Cold Spring Harbor Laboratory Press 2010
  • discovered via WithoutNotesMay11#DavidDeamer

Categories

• Biology

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