Agenda/Schedule
Click each agenda item's title for more information.
Evolving Chemical Systems
From Origins
Date/Time: November 13, 2019 - November 15, 2019
Location: Santa Fe Institute (Noyce Conference Room)
Organizers
David Baum (Univ. Wisconsin)
Oana Carja (Carnegie Mellon Univ.)
Chris Kempes (SFI)
Attendees
Celia Blanco (UC Santa Barbara)
Mark Ditzler (NASA)
Emily Dolson (Michigan State Univ.)
Steven Frank (UC Irvine)
Ben Kerr (Univ. Washington)
Samuel Levin (Oxford Univ.)
Omer Markovitch (Univ. Groningen)
Will Ratcliffe (Georgia Tech)
Sara Walker (Arizona State University)
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?
Additional Meeting Information
For this meeting, we would like everyone to consider the following list of questions:
- 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?
- If life starts with non-genetic modes of heritability (e.g., compositional), when, how and why might genetic encoding systems invade?
- What are missing components of current evolutionary theory and experimental design for realizing systems that can make the transition from chemistry to biology?
- When do changes in the dynamical state of a chemical system constitute analogs of development/succession, and when of evolution?
- 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?
Post-meeting Summary by Organizer[edit source]
Coming soon.
Additional Post-meeting Summary by Organizer
Post-meeting Reflection by Presenter
Post-meeting Reflection by Non-presenting Attendees
Key Reviews[edit source]
None.
Reference Materials by Presenting Attendees[edit source]
David Baum (Univ. Wisconsin)[edit source]
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) |
Celia Blanco (UC Santa Barbara)[edit source]
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 |
|---|---|---|---|---|---|---|
| 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 | 2 | Download (Encrypted) |
| 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 | 3 | Download (Encrypted) |
Mark Ditzler (NASA)[edit source]
| 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.)[edit source]
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)[edit source]
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) |
Ben Kerr (Univ. Washington)[edit source]
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 |
|---|---|---|---|---|---|---|
| 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 | 3 | Download (Encrypted) |
| 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 | 1 | Download (Encrypted) |
Samuel Levin (Oxford Univ.)[edit source]
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 |
|---|---|---|---|---|---|---|
| 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)[edit source]
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)[edit source]
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[edit source]
| Title | Author name | Source name | Year | Citation count From Scopus. Refreshed every 5 days. | Page views | Related file |
|---|---|---|---|---|---|---|
| Selforganization of matter and the evolution of biological macromolecules | Manfred Eigen | Die Naturwissenschaften | 1971 | 0 | 9 | Download (Encrypted) |
| Chemical Evolution and the Evolutionary Definition of Life | Paul G. Higgs | Journal of Molecular Evolution | 2017 | 0 | 4 | Download (Encrypted) |
| The Structure of Autocatalytic Sets: Evolvability, Enablement, and Emergence | Wim Hordijk, Mike Steel, Stuart Kauffman | Acta Biotheoretica | 2012 | 0 | 3 | Download (Encrypted) |
| Real ribozymes suggest a relaxed error threshold | Ádám Kun, Mauro Santos, Eörs Szathmáry | Nature Genetics | 2005 | 0 | 2 | 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 | 3 | Download (Encrypted) |
| The major evolutionary transitions | Eörs Szathmáry, John Maynard Smith | Nature | 1995 | 0 | 6 | 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) |
| 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) |
| Lipid vesicles chaperone an encapsulated RNA aptamer | Ranajay Saha, Samuel Verbanic, Irene A. Chen | Nature Communications | 2018 | 0 | 4 | Download (Encrypted) |
Discussion Forums
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