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

Evolving Chemical Systems

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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

    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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    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
    The origin and early evolution of life in chemical composition space David A. Baum Journal of Theoretical Biology 2018 0 13 Download (Encrypted)
    Selection and the Origin of Cells David A. Baum BioScience 2015 0 5 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 5 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
    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 2 Download (Encrypted)
    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 3 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
    Models of symbiosis Steven A. Frank American Naturalist 1997 0 4 Download (Encrypted)
    Natural selection. III. Selection versus transmission and the levels of selection S. A. Frank Journal of Evolutionary Biology 2012 0 2 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 evolution of cooperation in simple molecular replicators Samuel R. Levin, Stuart A. West Proceedings of the Royal Society B: Biological Sciences 2017 0 2 Download (Encrypted)
    The social coevolution hypothesis for the origin of enzymatic cooperation Samuel R. Levin, Sylvain Gandon, Stuart A. West 0 23 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
    Chemical Heredity as Group Selection at the Molecular Level Omer Markovitch, Olaf Witkowski, Nathaniel Virgo Molecular 2018 0 5 Download (Encrypted)
    Diversification of self-replicating molecules Jan W. Sadownik, Elio Mattia, Piotr Nowak, Sijbren Otto Nature Chemistry 2016 0 6 Download (Encrypted)
    Predicting species emergence in simulated complex pre-biotic networks Omer Markovitch, Natalio Krasnogor PLoS ONE 2018 0 4 Download (Encrypted)
    Quasispecies in population of compositional assemblies Renan Gross, Itzhak Fouxon, Doron Lancet, Omer Markovitch BMC Evolutionary Biology 2014 0 1 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
    Universal scaling across biochemical networks on Earth Hyunju Kim, Harrison B. Smith, Cole Mathis, Jason Raymond, Sara I. Walker Science Advances 2019 0 3 Download (Encrypted)
    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 1 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
    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 3 Download (Encrypted)
    Selforganization of matter and the evolution of biological macromolecules Manfred Eigen Die Naturwissenschaften 1971 0 9 Download (Encrypted)
    The major evolutionary transitions Eörs Szathmáry, John Maynard Smith Nature 1995 0 6 Download (Encrypted)
    Chemical Evolution and the Evolutionary Definition of Life Paul G. Higgs Journal of Molecular Evolution 2017 0 4 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 3 Download (Encrypted)
    The Structure of Autocatalytic Sets: Evolvability, Enablement, and Emergence Wim Hordijk, Mike Steel, Stuart Kauffman Acta Biotheoretica 2012 0 3 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 5 Download (Encrypted)
    Real ribozymes suggest a relaxed error threshold Ádám Kun, Mauro Santos, Eörs Szathmáry Nature Genetics 2005 0 2 Download (Encrypted)
    Lipid vesicles chaperone an encapsulated RNA aptamer Ranajay Saha, Samuel Verbanic, Irene A. Chen Nature Communications 2018 0 4 Download (Encrypted)

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