Systems Prebiology-Studies of the origin of Life
In the realm of prebiotic evolution, we have proposed a Lipid World model for life’s emergence, involving primordial assemblies of lipid-like amphiphilic molecules which can faithfully pass their compositional information to fission progeny. We have devised artificial chemistry formalism, the Graded Autocatalysis Replication Domain (GARD) model to test our hypothesis. The model describes, by computer simulations, the chemical dynamics in large molecular repertoires of prebiotic molecules. GARD depicts the biased accretion kinetics of molecular assemblies that are kept far from equilibrium by occasional fission.
Our simulations demonstrate the capacity of primordial transfer of “compositional genome” information. This implies a primitive self-replication mechanism, simpler than the ones involving nucleic acid sequence templating (“RNA world”). GARD analyses portray the formation of metabolism-like networks, analyzable by the tools of Systems Biology. We demonstrated that GARD network display the phenomenon of synthetic lethality, in which two non-lethal compositional mutations yield a lethal phenotype when combined. Recently, we found that when GARD’s network contain high levels of self-catalysis, this results in low diversity of its compositional “species” (compotypes) and a diminished ability to respond to external selection pressure. This suggests that self-copying of individual molecules, commonly taken as a unique prerequisite for life’s emergence, should be complemented with significant mutual catalysis for effective overall system’s evolvability. Presently, we study the behavior of GARD populations in terms of ecological predator-prey and cooperative interactions among species-like molecular assemblies (Figure). The above approaches show the centrality of tools related to the complexity of present-day life in understanding very early evolution. .
Figure: GARD dynamics
A. A typical similarity ‘carpet’ portraying the compositional similarity between all compositions encountered in a simulation. For simplicity, after each split only one child is followed and the other one is discarded. Compotypes are centers of mass of sets of faithfully replicating assemblies, appearing as red blocks along the diagonal.
B. An example of population dynamics, where a set with a fixed size of 1,000 assemblies is allowed to simultaneously grow based on their idiosyncratic composition. The population size is kept constant where after each split a random assembly is removed. Broken lines represent the four compotype species present in this simulation and solid lines are a fit to the logistic growth: dCi/dt=ri*Ci*[1-sum(aij*Cj)/Ki], where Ci is the fraction of compotype i in the population at time t, ri is the intrinsic growth rate, Ki is the environmental carrying capacity and aij reflects the competition between compotype j and i.
Markovitch O, Lancet D.
Excess Mutual Catalysis is Required For Effective Evolvability.
Artificial Life, 18(3):243-266 (2012)
Markovitch, Sorek, Lui, Lancet and Krasnogor
Is there an optimal level of open-endedness in prebiotic evolution?.
Origins of Life and Evolution of Biospheres 42, 469 (2012)
Armstrong, D.L., Markovitch, O., Zidovetzki, R. and Lancet, D.
Replication of simulated prebiotic amphiphile vesicles controlled by experimental lipid physicochemical properties.
Phys. Biol.8/398515 (2011)
Kafri, R., Markovitch, O. and Lancet, D.
Spontaneous chiral symmetry breaking in early molecular networks.
Biol Direct 5:38 (2010).
Inger, A., Solomon, A., Shenhav, B., Olender, T. and Lancet, D.
Mutations and Lethility in Simulated Prebiotic Networks.
J Mol Evol 69:568–578 (2009).
Shenhav , B., Oz, A. and Lancet, D.
Co-Evolution of compositional Protocells and their Environment.
Phil. Trans. R. Soc. B. 362 1813-1819. (2007).
Hunding,A., Kepes, F., Lancet, D., Minsky, A., Norris,V., Raine, D., Sriram, K., Root-Bernstein, R.
Compositional complementarity and prebiotic ecology in the origin of life.
Bioessays. 28(4): 399-412 (2006).
Barak Shenhav, Arren Bar-Even, Ran Kafri and Doron Lancet,Origins Life Evol. Polymer GARD: computer simulation of covalent bond formation in reproducing molecular assembliesBiosphere (2005), 35(2), 111-133. [PDF]
Shenhav, B., Solomon A., Lancet, D. and Kafri, R.
Early Systems Biology and Prebiotic Networks.
Transactions in Computational Systems Biology, LNBI 3380:14-17 (2005).[PDF]
Shenhav, B. and Lancet, D.
Prospects of a Computational Origin-of-life Endeavor (CORE).
Origins of Life and Evolution of the Biosphere. 34: 181-194 (2004).[PDF]
Kafri, R. and Lancet, D.
A probability rule for chiral recognition.
Chirality 16(6): 369-378 (2004).
Shenhav, B., Segre, D. and Lancet, D.
Mesobiotic emergence: molecular and assemble complexity and early evolution.
Advances in Complex Systems 6(1): 15-35 (2003). [PDF]
Segre, D., Ben-Eli, D., Deamer, D. and Lancet, D.
The lipid world.
Origins Life and Evol. Of the Biosphere, 31:119-145 (2001).[PDF]
Segre, D., Shenhav, B., Kafri, R. and Lancet, D.
The molecular roots of compositional inheritance.
Journal of Theoretical Biology. 213:481-491 (2001). [PDF]
Segre, D., Ben-Eli, D. and Lancet, D.
Compositional genomes: prebiotic information transfer in mutually catalytic non-covalent assemblies.
Proc. Natl. Acad. Sci (USA) 97 (8): 4112-4117 (2000). [PDF][Software & extras]
Segré, D., Lancet, D., Kedem, O. and Pilpel, Y.
Graded Autocatalysis Replication Domain (GARD): Kinetic Analysis of Self-Replication in Mutually Catalytic Sets.
Origins of Life and Evolution of the Biosphere, 28: 501-514 (1998).
Segré, D., Pilpel Y. and Lancet D.
Mutual catalysis in sets of prebiotic organic molecules: Evolution through computer simulated chemical kinetics.
Physica A (1998) 249, 558-564. [PDF]
Reviews and Book Chapters
• Markovitch, O., Inger, A., Shenhav, B. and Lancet, D.
Replication and Darwinian Selection Define Life’s Origin. In: Origin of Life and evolution of Biospheres. 40 (4-5) 484-488 (2010).
• Lancet, D. and Shenhav, B.
Compositional lipid protocells: reproduction without polynucleotides. In: Protocells: Bridging Nonliving and Living Matter. S. Rasmussen, M. A. Bedau, L. Chen, D. Deamer, D. C. Krakauer, N.H. Packard, & P. F. Stadler, Eds, MIT Press (2008).
• Arren Bar-Even, Barak Shenhav, Ran Kafri and Doron Lancet
The Lipid World: from catalytic and informational headgroups to micelle replication and evolution without nucleic acids.
J.Seckbach (ed), Life in the Universe,p111-114, Kluwer Academic Publishers, The Netherlands, 2005.[PDF]
• Naveh, B., Sipper, M., Lancet, D. and Shenhav, B.
Lipidia: An artificial chemistry of self-replicating assemblies of lipid-like molecules, in Artificial Life IX: Proceedings of the 9th International Conference on the Simulation and Synthesis of Living Systems, J. Pollack, M. Bedau, P. Husbands, T. Ikegami, and R. A. Watson, Eds., pp. 466-471, The MIT Press, Cambridge, Massachusetts (2004).
• Daniel Segre' and Doron Lancet
Theoretical and Computational Approaches to the Study of the Origin of Life
J.Seckbach (ed), Cellular Origin and Life in Extreme Habitats, 91-120, Kluwer Academic Publishers, The Netherlands, 2004. [PDF]
• Lancet, D. Computer simulation of protocells.
Computational Methods in Systems Biology.
Proceedings Lecture Notes in Computer Science. 2602: 194-197 (2003).
• Lancet, D.
Life without the double helix: Oparin revisited.
DNA 50: The Secret of Life - Celebrating the 50th Anniversary of the Double Helix Discovery. M. Balaban Ed., Faircount Publishers, p.126-135 (2003). [PDF]
• Segré, D. and Lancet, D.
A statistical chemistry approach to the origin of life.
Origins of Life Special Issue, Geoffrey Zubay, Ed. Chemtracts- Biochemistry and Molecular Biology, 12(6): 382-397 (1999). [PDF]
• Lancet, D., Glusman, G., Segré, D., Kedem, O. and Pilpel, Y.
Self-Replication and Chemical Selection in Primordial Mutually Catalytic Sets.
Origins of Life and Evolution of the Biosphere, 26: 270-271 (1996).
• D.Segre', D.Ben-Eli and D.Lancet
Prebiotic evolution of amphiphilic assemblies far from equilibrium: from compositional information to sequence-based biopolymers.
Bioastronomy 99: A New Era in the Search for Life. [PDF]
• D.Segre' and Lancet D.
Mutually catalytic amphiphiles: simulated chemical evolution and implications to exobiology.
J.Chela-Flores and F.Raulin (eds), Exobiology: Matter, Energy and Information in the Origin and Evolution of Life in the Universe, 123-131, Kluwer Academic Publishers, The Netherlands, 1998. [PDF]
• Segre' D., Pilpel Y., Glusman G. and Lancet D.
Self-replication and evolution in primordial mutually catalytic set
C. B. Cosmovici, S. Bowyer, D. Werthimer, Astronomical and Biochemical Origins and the Search for Life in the Universe, Editrice Compositori, Bologna, 1997, 469-476. [PDF]
• Barak Shenhav, Ran Kafri and Doron Lancet.
Graded Artificial Chemistry in Restricted Boundaries
Proceeding of the 9th International Conference on the Simulation and Synthesis of Living Systems (ALIFE9), Boston, Massachusetts, 501-506.
Graded Artificial Chemistry in Restricted Boundaries. [PDF]
• Barak Naveh, Moshe Sipper, Doron Lancet and Barak Shenhav
Lipidia: An Artificial Chemistry of Self-Replicating Assemblies of Lipid-like Molecules
Proceeding of the 9th International Conference on the Simulation and Synthesis of Living Systems (ALIFE9), Boston, Massachusetts, 466-471. [PDF]
• Daniel Segre', Dafna Ben-Eli, Yitzhak Pilpel, Ora Kedem and Doron Lancet
GARDobes: Primordial cell nano-precursors with organic catalysis, compositional genome and capacity to evolve
In Instruments, Methods, and Missions for Astrobiology II, Richard B. Hoover, Ed., Proceedings of SPIE, Vol.3755, 144-162 (1999) [PDF]