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Contact: Chris Kempes, Project Principal Investigator, ckempes@santafe.edu

Difference between revisions of "Evolving Chemical Systems"

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# Origin of life theory often invokes “autocatalysis,” but there are many kinds invoked (e.g., RNA-complement templating; hypercycles; RAF sets; branched-networks like the rTCA). What kind(s) of autocatalytic mechanisms are easiest to imagine arising spontaneously? What kind(s) are most amenable to evolving towards life-like complexity?
 
# Origin of life theory often invokes “autocatalysis,” but there are many kinds invoked (e.g., RNA-complement templating; hypercycles; RAF sets; branched-networks like the rTCA). What kind(s) of autocatalytic mechanisms are easiest to imagine arising spontaneously? What kind(s) are most amenable to evolving towards life-like complexity?
 
|Attendee list=CeliaBlanco;MarkDitzler;EmilyDolson;StevenFrank;BenKerr;SamuelLevine;OmerMarkovitch;WillRatcliffe;SaraWalker
 
|Attendee list=CeliaBlanco;MarkDitzler;EmilyDolson;StevenFrank;BenKerr;SamuelLevine;OmerMarkovitch;WillRatcliffe;SaraWalker
 +
|Student list=WikiWorks4
 
}}
 
}}

Revision as of 15:03, November 4, 2019


Date/Time: November 13, 2019 - November 15, 2019


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Organizers

  • David Baum (Univ. Wisconsin)

  • Oana Carja (Carnegie Mellon Univ.)

  • Chris Kempes (SFI)

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    Attendees
    Students

    Agenda/Schedule
    Click each agenda item's title for more information.
    Wednesday, November 13, 2019
    8:15 am - 8:30 am Day 1 Shuttle Departing Hotel Santa Fe (at lobby) to SFI
    8:30 am - 9:00 am Arrival, Breakfast, and Introductions
    9:00 am - 9:30 am Overview of the meeting and foundational concepts - Chris Kempes (SFI)
    9:30 am - 10:00 am Talk 1 + Large Group Discussion - Oana Carja (Carnegie Mellon Univ.)
    10:00 am - 10:30 am Talk 2 + Large Group Discussion - David Baum (Univ. Wisconsin)
    10:30 am - 11:00 am Talk 3 + Large Group Discussion - Sara Walker (Arizona State University)
    11:00 am - 11:15 am Day 1 AM Break
    11:15 am - 11:45 am Talk 4 + Large Group Discussion - Mark Ditzler (NASA)
    11:45 am - 12:15 pm Talk 5 + Large Group Discussion - Emily Dolson (Michigan State Univ.)
    12:15 pm - 1:00 pm Day 1 Lunch
    1:00 pm - 1:30 pm Talk 6 + Large Group Discussion - Celia Blanco (UC Santa Barbara)
    1:30 pm - 2:00 pm Talk 7 + Large Group Discussion - Omer Markovitch (Univ. Groningen)
    2:00 pm - 2:30 pm Talk 8 + Large Group Discussion - Will Ratcliffe (Georgia Tech)
    2:30 pm - 3:00 pm Talk 9 + Large Group Discussion - Steven Frank (UC Irvine)
    3:00 pm - 3:30 pm Talk 10 + Large Group Discussion - Samuel Levin (Oxford Univ.)
    3:30 pm - 3:45 pm Day 1 PM Break
    3:45 pm - 4:15 pm Talk 11 + Large Group Discussion - Ben Kerr (Univ. Washington)
    4:15 pm - 5:00 pm Large Group Discussion - Organizing the activities and priorities of the working group (based on talks and discussions)
    5:15 pm Day 1 Shuttle Departing SFI to Hotel Santa Fe
    6:30 pm Group dinner
    Thursday, November 14, 2019
    8:15 am - 8:30 am Day 2 Shuttle Departing Hotel Santa Fe (at lobby) to SFI
    8:30 am - 9:00 am Day 2 Arrival and Breakfast
    9:00 am - 9:25 am Large Group Discussion - Breakout Group Proposals
    9:25 am - 11:25 am Breakout Group Discussion 1
    11:25 am - 11:45 am Large Group Discussion - Recap from the breakout groups
    11:45 am - 12:00 pm Wiki platform walk through - Amy P Chen (SFI)
    12:00 pm - 1:30 pm Day 2 Lunch
    1:30 pm - 2:30 pm Large Group Discussion - Synthesis and next steps
    2:30 pm - 4:30 pm Breakout Group Discussion 2
    4:30 pm - 5:00 pm Large Group Discussion - Plan for Day 3
    5:15 pm Day 2 Shuttle Departing SFI to Hotel Santa Fe
    Friday, November 15, 2019
    8:15 am - 8:30 am Day 3 Shuttle Departing Hotel Santa Fe (at lobby) to SFI
    8:30 am - 9:00 am Day 3 Arrival and Breakfast
    9:00 am - 12:00 pm AM TBD (will decide based on Day 2)
    12:00 pm - 1:00 pm Day 3 Lunch
    1:00 pm - 5:00 pm PM TBD (will decide based on Day 2)
    5:15 pm Day 3 Shuttle Departing SFI to Hotel Santa Fe

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    Meeting Synopsis

    The goal of this working group is to address the onset of adaptive evolution in a prebiotic context. What theories or models of evolution allow selection-like processes to begin prior to genetic inheritance systems, and what spatial contexts do these models require (from well-mixed systems, to 2D-arrays, to protocells)?  We will discuss existing theories, as well as needed evolutionary frameworks to understand how chemical systems became biological systems. Can we use evolutionary theory to guide the design of experiments aimed at understanding how systems become capable of making the transition from the abiotic to biotic?

    For this meeting, we would like everyone to consider the following list of questions:

    1. What theories or models of evolution allow selection-like processes to begin prior to genetic inheritance systems? What spatial contexts do these models require (from well-mixed systems, to 2D-arrays, to protocells, to systems with different rates of diffusion for different classes of molecule)? How important is spatial structure within this context?
    2. If life starts with non-genetic modes of heritability (e.g., compositional), when, how and why might genetic encoding systems invade?
    3. What are missing components of current evolutionary theory and experimental design for realizing systems that can make the transition from chemistry to biology?
    4. When do changes in the dynamical state of a chemical system constitute analogs of development/succession, and when of evolution?
    5. Origin of life theory often invokes “autocatalysis,” but there are many kinds invoked (e.g., RNA-complement templating; hypercycles; RAF sets; branched-networks like the rTCA). What kind(s) of autocatalytic mechanisms are easiest to imagine arising spontaneously? What kind(s) are most amenable to evolving towards life-like complexity?

    Key Reviews

    None.

    Reference Materials by Presenting Attendees

    David Baum (Univ. Wisconsin)

    A paper of mine related to this meeting (an easy read!)

    Title Author name Source name Year Citation count From Scopus. Refreshed every 5 days. Page views Related file
    Selection and the Origin of Cells David A. Baum BioScience 2015 0 0 Download (Encrypted)
    Effects of spatial diffusion on nonequilibrium steady states in a model for prebiotic evolution B. F. Intoy, A. Wynveen, J. W. Halley Physical Review E 2016 0 0 Download (Encrypted)
    Nonequilibrium steady states in a model for prebiotic evolution A. Wynveen, I. Fedorov, J. W. Halley Physical Review E - Statistical, Nonlinear, and Soft Matter Physics 2014 0 0 Download (Encrypted)
    The origin and early evolution of life in chemical composition space David A. Baum Journal of Theoretical Biology 2018 0 0 Download (Encrypted)

    Celia Blanco (UC Santa Barbara)

    Two most relevant paper of mine to this WG.

    Title Author name Source name Year Citation count From Scopus. Refreshed every 5 days. Page views Related file
    Mapping a Systematic Ribozyme Fitness Landscape Reveals a Frustrated Evolutionary Network for Self-Aminoacylating RNA Abe D. Pressman, Ziwei Liu, Evan Janzen, Celia Blanco, Ulrich F. Müller, Gerald F. Joyce, Robert Pascal, Irene A. Chen Journal of the American Chemical Society 2019 0 0 Download (Encrypted)
    Mirror symmetry breaking with limited enantioselective autocatalysis and temperature gradients: A stability survey Celia Blanco, Josep M. Ribó, Joaquim Crusats, Zoubir El-Hachemi, Albert Moyano, David Hochberg Physical Chemistry Chemical Physics 2013 0 0 Download (Encrypted)

    Mark Ditzler (NASA)

    Title Author name Source name Year Citation count From Scopus. Refreshed every 5 days. Page views Related file
    Self-assembling amphiphilic molecules: Synthesis in simulated interstellar/precometary ices Jason P. Dworkin, David W. Deamer, Scott A. Sandford, Louis J. Allamandola Proceedings of the National Academy of Sciences of the United States of America 2001 0 0 Download

    Emily Dolson (Michigan State Univ.)

    The MODES Toolbox paper provides some background on what Open-Ended Evolution is and how to measure it.

    The ecology and evolutionary computation paper provides more detail on the ecological networks I showed at the end of my talk.

    Title Author name Source name Year Citation count From Scopus. Refreshed every 5 days. Page views Related file
    The MODES toolbox: Measurements of open-ended dynamics in evolving systems Emily L. Dolson, Anya E. Vostinar, Michael J. Wiser, Charles Ofria Artificial Life 2019 0 0 Download (Encrypted)
    Ecological theory provides insights about evolutionary computation Emily Dolson, Charles Ofria GECCO 2018 Companion - Proceedings of the 2018 Genetic and Evolutionary Computation Conference Companion 2018 0 0 Download (Encrypted)

    Steven Frank (UC Irvine)

    Two most relevant paper of mine to this WG.

    Title Author name Source name Year Citation count From Scopus. Refreshed every 5 days. Page views Related file
    Natural selection. III. Selection versus transmission and the levels of selection S. A. Frank Journal of Evolutionary Biology 2012 0 0 Download (Encrypted)
    Models of symbiosis Steven A. Frank American Naturalist 1997 0 0 Download (Encrypted)

    Ben Kerr (Univ. Washington)

    Two paper of mine related to this meeting.

    Title Author name Source name Year Citation count From Scopus. Refreshed every 5 days. Page views Related file
    Evolution of restraint in a structured rock-paper-scissors community Joshua R. Nahum, Brittany N. Harding, Benjamin Kerr Proceedings of the National Academy of Sciences of the United States of America 2011 0 0 Download (Encrypted)
    The Evolutionary Origin of Somatic Cells under the Dirty Work Hypothesis Heather J. Goldsby, David B. Knoester, Charles Ofria, Benjamin Kerr PLoS Biology 2014 0 0 Download (Encrypted)

    Samuel Levin (Oxford Univ.)

    Title Author name Source name Year Citation count From Scopus. Refreshed every 5 days. Page views Related file
    The social coevolution hypothesis for the origin of enzymatic cooperation Samuel R. Levin, Sylvain Gandon, Stuart A. West 0 0 Download (Encrypted)
    The evolution of cooperation in simple molecular replicators Samuel R. Levin, Stuart A. West Proceedings of the Royal Society B: Biological Sciences 2017 0 0 Download (Encrypted)

    Omer Markovitch (Univ. Groningen)

    1) Markovitch et al. 2018: Addressing the 'bridge' between chemistry and biology by trying to apply biological tool on a chemical system showing replication.

    2) Markovitch & Krasnogor, 2018: Demonstrates how a network can be analyzed in order to extract all potential 'species', in a dynamical context.

    3) Gross et al. 2014: Shows how compositional replicators could be cast in terms of Eigen's Quasispecies, hence in principle are evolvable in the same way a quasispecies is.

    4) Sadownik et al. 2016; An experimental system based on multiple (two) types of building block showed not only the emergence of a variety of replicators but also that some of these replicators emerged with the help of other replicators.

    Title Author name Source name Year Citation count From Scopus. Refreshed every 5 days. Page views Related file
    Diversification of self-replicating molecules Jan W. Sadownik, Elio Mattia, Piotr Nowak, Sijbren Otto Nature Chemistry 2016 0 0 Download (Encrypted)
    Predicting species emergence in simulated complex pre-biotic networks Omer Markovitch, Natalio Krasnogor PLoS ONE 2018 0 0 Download (Encrypted)
    Quasispecies in population of compositional assemblies Renan Gross, Itzhak Fouxon, Doron Lancet, Omer Markovitch BMC Evolutionary Biology 2014 0 0 Download (Encrypted)
    Chemical Heredity as Group Selection at the Molecular Level Omer Markovitch, Olaf Witkowski, Nathaniel Virgo Molecular 2018 0 0 Download (Encrypted)

    Sara Walker (Arizona State University)

    Two most relevant paper of mine to this WG.

    Title Author name Source name Year Citation count From Scopus. Refreshed every 5 days. Page views Related file
    Environmental control programs the emergence of distinct functional ensembles from unconstrained chemical reactions Andrew J. Surman, Marc Rodriguez-Garcia, Yousef M. Abul-Haija, Geoffrey J.T. Cooper, Piotr S. Gromski, Rebecca Turk-MacLeoda, Margaret Mullin, Cole Mathis, Sara I. Walker, Leroy Cronin Proceedings of the National Academy of Sciences of the United States of America 2019 0 0 Download (Encrypted)
    Universal scaling across biochemical networks on Earth Hyunju Kim, Harrison B. Smith, Cole Mathis, Jason Raymond, Sara I. Walker Science Advances 2019 0 0 Download (Encrypted)
    Reference Materials by Non-presenting Attendees


    General Meeting Reference Material

    Title Author name Source name Year Citation count From Scopus. Refreshed every 5 days. Page views Related file
    Chemical Evolution and the Evolutionary Definition of Life Paul G. Higgs Journal of Molecular Evolution 2017 0 0 Download (Encrypted)
    Multilevel selection in models of prebiotic evolution II: A direct comparison of compartmentalization and spatial self-organization Nobuto Takeuchi, Paulien Hogeweg PLoS Computational Biology 2009 0 0 Download (Encrypted)
    The Structure of Autocatalytic Sets: Evolvability, Enablement, and Emergence Wim Hordijk, Mike Steel, Stuart Kauffman Acta Biotheoretica 2012 0 0 Download (Encrypted)
    Prevolutionary dynamics and the origin of evolution Martin A. Nowak, Hisashi Ohtsuki Proceedings of the National Academy of Sciences of the United States of America 2008 0 0 Download (Encrypted)
    Real ribozymes suggest a relaxed error threshold Ádám Kun, Mauro Santos, Eörs Szathmáry Nature Genetics 2005 0 0 Download (Encrypted)
    Lipid vesicles chaperone an encapsulated RNA aptamer Ranajay Saha, Samuel Verbanic, Irene A. Chen Nature Communications 2018 0 0 Download (Encrypted)
    Compositional genomes: Prebiotic information transfer in mutually catalytic noncovalent assemblies Daniel Segré, Dafna Ben-Eli, Doron Lancet Proceedings of the National Academy of Sciences of the United States of America 2000 0 0 Download (Encrypted)
    Selforganization of matter and the evolution of biological macromolecules Manfred Eigen Die Naturwissenschaften 1971 0 0 Download (Encrypted)
    The major evolutionary transitions Eörs Szathmáry, John Maynard Smith Nature 1995 0 0 Download (Encrypted)

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