Prebiotic Evolution of Molecular Assemblies: From Molecules to Ecology

1. Prebiotic Evolution of Molecular Assemblies: From Molecules to Ecology Omer Markovitch and Doron Lancet Department of Molecular Genetics, Weizmann Institute of Science, Israel

2. Metabolism Eco-system

3. Lipid world RNA world Assemblies / Clusters / Vesicles / Membranes  Composition non-covalent bonds DNA / RNA / Polymers  Sequence covalent bonds Segre and Lancet, EMBO Reports 1 (2000)

4. GARD model (Graded Autocatalysis Replication Domain) • Synthetic chemistry • Kinetic model • Catalytic network (b) of rate-enhancement values Homeostatic growth b Fission / Split Rate enhancement Molecular repertoire Segre, Ben-Eli and Lancet, Proc. Natl. Acad. Sci. 97 (2000)

5. b ; Catalytic Network (environmental chemistry) b NG = 100 bij “Metabolic” network More selfish More mutualistic

6. GARD model (Graded Autocatalysis Replication Domain) Following a single lineage. Composome (compositional genome) = a faithfully replicating composition/assembly. Compotype (composome type) = a collection of similar composomes  quasispecies. Similarity ‘carpet’ Compositional Similarity

7. Present-day organism – Complex From organisms to food webs –Complex Prebiotic Ecology: From molecules to Ecosystem. ( from species inner structure to food web)

8. Population Dynamics in GARD Following the dynamics of a constant-size population of assemblies. Buffered environment (=unlimited food). At each time point, each assembly is colored by its compotype. Member of population 8

9. Population Dynamics in GARD Simulations exhibiting a single compotype species: One example Another example Each simulation with a different chemistry (b network). 9

10. Population Dynamics in GARD Simulations exhibiting multiple compotypes: One example Another example Each simulation with a different chemistry (b network). 10

11. Logistic Growth [Gause (1934)] Independently cultivated Lotka-Volterra 0 10 15 20 10-6 m 5 C = compotype frequency in the population r = compotype intrinsic growth rate K = compotype carrying capacity a = competition parameters between two species 11

12. Population Dynamics in GARD <<Data removed from published version>>

13. Why plateau is lower than 1.0 ? <<Data removed from published version>>

14. GARD’s Ecology Compotype sub-network part of b <<Data removed from published version>> 14

15. GARD’s Ecology Correlation = -0.38 P-value = 0.000031 Based on experimental data of 111 bacteria. Freilich et al, Genome Biology (2009) 15

16. Population Dynamics in GARD “Takeover” of a fast-rising compotype by a slower one. <<Data removed from published version>>

17. Population Dynamics in GARD 17

18. Lipid-world & GARD model: compositional assemblies • Compotypes (clusters of faithfully replicating compositions) • Populations dynamics • Logistic behavior • Species competition, takeover • Molecular parameters  Population ecology • Carrying capacity (K) • Molecular repertoire effects r & K

19. Complicated Simple

20. Acknowledgements: Doron Lancet. Avi Mayo (Weizmann). Raphael Zidovetzki (U. California Riverside, USA). NatalioKrasnogor (U. Nottingham, UK). Lancet group. Funding: * Minerva Center for Life Under Extreme Planetary Conditions, at Weizmann Institute. * E.U. FP7 “MATCHIT”. Omer Markovitch

21. Selection in GARD Selection of GARD assemblies towards a target compotype. Negative Positive GARD portrays selection. 21 Markovitch and Lancet, Artificial Life 18:3 (2012)

22. Lack of selectivity in GARD? NO. Vasas, Szathmary & Santos, PNAS 107, 1470-1475 (2010): Imposing Darwinian selection in GARD has, at most, negligible effect… –– Regular –– Beneficial –– Detrimental Frequency • Their weak points: • Target is not a composome. • Only a single simulation performed. • Small repertoire (NG=10) and assembly size (Nmax=6). • Arbitrary fitness threshold. Index of assembly composition