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

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

5.  ; Catalytic Network (environmental chemistry) More mutualistic More selfish  N G = 100  ij “Metabolic” network

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

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 8 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

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

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

11. 11 Logistic Growth C = compotype frequency in the population r = compotype intrinsic growth rate K = compotype carrying capacity  = competition parameters between two species [Gause (1934)] Independently cultivated 0 5 101520 Lotka-Volterra 10 -6 m

12. Population Dynamics in GARD >

13. Why plateau is lower than 1.0 ? >

14. GARD’s Ecology 14 Compotype sub-network  part of  >

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

16. Population Dynamics in GARD “Takeover” of a fast- rising compotype by a slower one. >

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. Simple Complicated

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

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

22. Lack of selectivity in GARD? NO. Their weak points: (1)Target is not a composome. (2)Only a single simulation performed. (3)Small repertoire (N G =10) and assembly size (N max =6). (4)Arbitrary fitness threshold. Index of assembly composition Frequency Vasas, Szathmary & Santos, PNAS 107, 1470-1475 (2010): Imposing Darwinian selection in GARD has, at most, negligible effect… –– Regular –– Beneficial –– Detrimental 22