Coevolution of compositional protocells and their environment
Open accessAbstract
The coevolution of environment and living organisms is well known in nature. Here, it is suggested that similar processes can take place before the onset of life, where protocellular entities, rather than full-fledged living systems, coevolve along with their surroundings. Specifically, it is suggested that the chemical composition of the environment may have governed the chemical repertoire generated within molecular assemblies, compositional protocells, while compounds generated within these protocells altered the chemical composition of the environment. We present an extension of the graded autocatalysis replication domain (GARD) model—the environment exchange polymer GARD (EE-GARD) model. In the new model, molecules, which are formed in a protocellular assembly, may be exported to the environment that surrounds the protocell. Computer simulations of the model using an infinite-sized environment showed that EE-GARD assemblies may assume several distinct quasi-stationary compositions (composomes), similar to the observations in previous variants of the GARD model. A statistical analysis suggested that the repertoire of composomes manifested by the assemblies is independent of time. In simulations with a finite environment, this was not the case. Composomes, which were frequent in the early stages of the simulation disappeared, while others emerged. The change in the frequencies of composomes was found to be correlated with changes induced on the environment by the assembly. The EE-GARD model is the first GARD model to portray a possible time evolution of the composomes repertoire.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
A simulation under constant population conditions showed the dynamics of takeover and extinction of dimer-containing composomes.
“A simulation under constant population conditions showed the dynamics of takeover and extinction of dimer-containing composomes [58].”
From Systems protobiology: origin of life in lipid catalytic networks (2018) · cites this paper as [58]
Cites
Gillespie, D. T. (1976) · Journal of Computational Physics · doi:10.1016/0021-9991(76)90041-3 · Cited by 6,029 · see citing works
Szostak, J. W., Bartel, D. P., & Luisi, P. L. (2001) · Nature · doi:10.1038/35053176 · Cited by 1,681 · see citing works
The U.S. Carbon Budget: Contributions from Land-Use Change
Houghton, R. A., Hackler, J. L., & Lawrence, K. T. (1999) · Science · doi:10.1126/science.285.5427.574 · Cited by 1,136 · see citing works
Man-made cell-like compartments for molecular evolution
Tawfik, D. S., & Griffiths, A. D. (1998) · Nature Biotechnology · doi:10.1038/nbt0798-652 · Cited by 960 · see citing works
Experimental Models of Primitive Cellular Compartments: Encapsulation, Growth, and Division
Hanczyc, M. M., Fujikawa, S. M., & Szostak, J. W. (2003) · Science · doi:10.1126/science.1089904 · Cited by 848 · see citing works
Just, T., Oparin, A. I., & Morgulis, S. (1938) · The American Midland Naturalist · doi:10.2307/2420646 · Cited by 626 · see citing works
Segré, D., Ben-Eli, D., Deamer, D. W., & Lancet, D. (2001) · Origins of life and evolution of the biosphere · doi:10.1023/a:1006746807104 · Cited by 620 · see citing works
Self-citationCompositional genomes: Prebiotic information transfer in mutually catalytic noncovalent assemblies
Segré, D., Ben-Eli, D., & Lancet, D. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.97.8.4112 · Cited by 398 · see citing works
Self-citationWhen Did Photosynthesis Emerge on Earth?
Marais, D. J. D. (2000) · Science · doi:10.1126/science.289.5485.1703 · Cited by 390 · see citing works
How Earth's atmosphere evolved to an oxic state: A status report
Catling, D. C., & Claire, M. W. (2005) · Earth and Planetary Science Letters · doi:10.1016/j.epsl.2005.06.013 · Cited by 376 · see citing works
Membrane self‐assembly processes: Steps toward the first cellular life
Monnard, P., & Deamer, D. W. (2002) · The Anatomical Record · doi:10.1002/ar.10154 · Cited by 319 · see citing works
Bridging Nonliving and Living Matter
Rasmussen, S., Chen, L., Nilsson, M., & Abe, S. (2003) · Artificial Life · doi:10.1162/106454603322392479 · Cited by 266 · see citing works
Sea ice as the glacial cycles’ Climate switch: role of seasonal and orbital forcing
Gildor, H., & Tziperman, E. (2000) · Paleoceanography · doi:10.1029/1999pa000461 · Cited by 208 · see citing works
Lancet, D., Sadovsky, E., & Seidemann, E. (1993) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.90.8.3715 · Cited by 160 · see citing works
Self-citationSegré, D., & Lancet, D. (2000) · The EMBO Reports · doi:10.1093/embo-reports/kvd063 · Cited by 133 · see citing works
Self-citationSegrè, D., Lancet, D., Kedem, O., & Pilpel, Y. (1998) · Origins of Life and Evolution of Biospheres · doi:10.1023/a:1006583712886 · Cited by 126 · see citing works
Self-citationSea-ice switches and abrupt climate change
Gildor, H., & Tziperman, E. (2003) · Philosophical Transactions of the Royal Society A Mathematical Physical and Engineering Sciences · doi:10.1098/rsta.2003.1244 · Cited by 112 · see citing works
The Molecular Roots of Compositional Inheritance
SEGRÉ, D., SHENHAV, B., KAFRI, R., & LANCET, D. (2001) · Journal of Theoretical Biology · doi:10.1006/jtbi.2001.2440 · Cited by 82 · see citing works
Self-citationBiological Self-Replicating Systems
Morowitz, H. J. (1967) · Elsevier eBooks · doi:10.1016/b978-1-4831-9994-8.50009-0 · Cited by 71 · see citing works
Segerstråle, U. (2000) · Science · doi:10.1126/science.290.5497.1703 · Cited by 49 · see citing works
Master equations for random walks with arbitrary pausing time distributions
Gillespie, D. T. (1977) · Physics Letters A · doi:10.1016/0375-9601(77)90513-8 · Cited by 40 · see citing works
Test of a Statistical Model for Molecular Recognition in Biological Repertoires
ROSENWALD, S., KAFRI, R., & LANCET, D. (2002) · Journal of Theoretical Biology · doi:10.1006/jtbi.2002.2538 · Cited by 37 · see citing works
Self-citationMESOBIOTIC EMERGENCE: MOLECULAR AND ENSEMBLE COMPLEXITY IN EARLY EVOLUTION
SHENHAV, B., SEGRÈ, D., & LANCET, D. (2003) · Advances in Complex Systems · doi:10.1142/s0219525903000785 · Cited by 37 · see citing works
Self-citationPolymer Gard: Computer Simulation of Covalent Bond Formation in Reproducing Molecular Assemblies
Shenhav, B., Bar-Even, A., Kafri, R., & Lancet, D. (2005) · Origins of Life and Evolution of Biospheres · doi:10.1007/s11084-005-5578-z · Cited by 33 · see citing works
Self-citationLancet, D., Kedem, O., & Pilpel, Y. (1994) · Berichte der Bunsengesellschaft für physikalische Chemie · doi:10.1002/bbpc.19940980919 · Cited by 23 · see citing works
Self-citationThe origin of life on the earth / Translated from the Russian by Ann Synge.
Опарин, А. И., & Synge, A. (1957) · Academic Press eBooks · doi:10.5962/bhl.title.4528 · Cited by 14 · see citing works
Early Systems Biology and Prebiotic Networks
Shenhav, B., Solomon, A., Lancet, D., & Kafri, R. (2005) · Lecture Notes in Computer Science · doi:10.1007/978-3-540-32126-2_2 · Cited by 13 · see citing works
Self-citationGraded Artificial Chemistry in Restricted Boundaries
Shenhav, B., Kafri, R., & Lancet, D. (2004) · The MIT Press eBooks · doi:10.7551/mitpress/1429.003.0085 · Cited by 8 · see citing works
Self-citationLipidia: An Artificial Chemistry of Self-Replicating Assemblies of Lipid-like Molecules
Pollack, J. B., Bedau, M. A., Husbands, P., Watson, R. A. R., & Ikegami, T. (2004) · Cited by 7 · see citing works
Lipidia: An Artificial Chemistry of Self-Replicating Assemblies of Lipid-like Molecules
Naveh, B., Sipper, M., Lancet, D., & Shenhav, B. (2004) · Artificial Life IX · doi:10.7551/mitpress/1429.003.0079 · Cited by 4 · see citing works
Self-citation
Flagged first, then by citations
1 of the 31 references couldn’t be matched to a known paper.
Cited by
Sorted by citations
Vasas, V., Szathmáry, E., & Santos, M. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0912628107 · Cited by 196 · see citing works
Systems protobiology: origin of life in lipid catalytic networks
Lancet, D., Zidovetzki, R., & Markovitch, O. (2018) · Journal of The Royal Society Interface · doi:10.1098/rsif.2018.0159 · Cited by 182 · see citing works
Self-citationExcess mutual catalysis is required for effective evolvability
Markovitch, O., & Lancet, D. (2012) · Artificial Life · doi:10.1162/artl_a_00064 · Cited by 68 · see citing works
Self-citationMultispecies population dynamics of prebiotic compositional assemblies
Markovitch, O., & Lancet, D. (2014) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2014.05.005 · Cited by 43 · see citing works
Self-citationCoenzyme Autocatalytic Network on the Surface of Oil Microspheres as a Model for the Origin of Life
Sharov, A. A. (2009) · International Journal of Molecular Sciences · doi:10.3390/ijms10041838 · Cited by 37 · see citing works
Sharov, A. A., & Gordon, R. (2018) · Elsevier eBooks · doi:10.1016/b978-0-12-811940-2.00011-3 · Cited by 37 · see citing works
A Modular Hierarchy-Based Theory of the Chemical Origins of Life Based on Molecular Complementarity
Root-Bernstein, R. S. (2012) · Accounts of Chemical Research · doi:10.1021/ar200209k · Cited by 30 · see citing works
Spontaneous chiral symmetry breaking in early molecular networks
Kafri, R., Markovitch, O., & Lancet, D. (2010) · Biology Direct · doi:10.1186/1745-6150-5-38 · Cited by 28 · see citing works
Self-citationAn evolutionary process without variation and selection
Gabora, L., & Steel, M. (2021) · Journal of The Royal Society Interface · doi:10.1098/rsif.2021.0334 · Cited by 23 · see citing works
Quasispecies in population of compositional assemblies
Gross, R., Fouxon, I., Lancet, D., & Markovitch, O. (2014) · BMC Evolutionary Biology · doi:10.1186/s12862-014-0265-1 · Cited by 20 · see citing works
Self-citationCompositional Inheritance: Comparison of Self-assembly and Catalysis
Wu, M., & Higgs, P. G. (2008) · Origins of Life and Evolution of Biospheres · doi:10.1007/s11084-008-9143-4 · Cited by 19 · see citing works
Predicting species emergence in simulated complex pre-biotic networks
Markovitch, O., & Krasnogor, N. (2018) · PLOS ONE · doi:10.1371/journal.pone.0192871 · Cited by 19 · see citing works
Mathematical modeling of a minimal protocell with coordinated growth and division
Surovtsev, I. V., Zhang, Z., Lindahl, P. A., & Morgan, J. J. (2009) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2009.06.001 · Cited by 16 · see citing works
Mutations and Lethality in Simulated Prebiotic Networks
Inger, A., Solomon, A., Shenhav, B., Olender, T., & Lancet, D. (2009) · Journal of Molecular Evolution · doi:10.1007/s00239-009-9281-y · Cited by 14 · see citing works
Self-citationSpitzer, J. J. (2013) · Astrobiology · doi:10.1089/ast.2012.0924 · Cited by 14 · see citing works
Prebiological Evolution and the Metabolic Origins of Life
Pratt, A. J. (2011) · Artificial Life · doi:10.1162/artl_a_00032 · Cited by 13 · see citing works
Is There an Optimal Level of Open-Endedness in Prebiotic Evolution?
Markovitch, O., Sorek, D., Lui, L. T., Lancet, D., & Krasnogor, N. (2012) · Origins of Life and Evolution of Biospheres · doi:10.1007/s11084-012-9309-y · Cited by 13 · see citing works
Self-citationPeriyasamy, S., Gray, A. W., & Kille, P. (2008) · IEEE Congress on Evolutionary Computation (CEC) · doi:10.1109/cec.2008.4631235 · Cited by 13 · see citing works
Composite Agency: Semiotics of Modularity and Guiding Interactions
Sharov, A. A. (2017) · Biosemiotics · doi:10.1007/s12304-017-9301-z · Cited by 11 · see citing works
The Divergence and Natural Selection of Autocatalytic Primordial Metabolic Systems
Алексеевич, М. С., & Belonogova, O. V. (2013) · Origins of Life and Evolution of Biospheres · doi:10.1007/s11084-013-9340-7 · Cited by 11 · see citing works
The fats of the matter: Lipids in prebiotic chemistry and in origin of life studies
Santos, T. C. B., & Futerman, A. H. (2023) · Progress in Lipid Research · doi:10.1016/j.plipres.2023.101253 · Cited by 9 · see citing works
Armstrong, D. L., Markovitch, O., Zidovetzki, R., & Lancet, D. (2011) · Physical Biology · doi:10.1088/1478-3975/8/6/066001 · Cited by 9 · see citing works
Self-citationBuds of the tree: the highway to the last universal common ancestor
de Farías, S. T., & Prosdocimi, F. (2016) · International Journal of Astrobiology · doi:10.1017/s147355041600029x · Cited by 8 · see citing works
The origin of genetic and metabolic systems: Evolutionary structuralinsights
Deng, S. (2023) · Heliyon · doi:10.1016/j.heliyon.2023.e14466 · Cited by 7 · see citing works
The Emergence of the First Cells
Danchin, A. (2014) · Wiley-VCH eBooks · doi:10.1002/3527600906.mcb.20130025 · Cited by 6 · see citing works
Kurisu, M., & Imai, M. (2023) · Biophysics and Physicobiology · doi:10.2142/biophysico.bppb-v21.0002 · Cited by 4 · see citing works
Das, S., Pal, R., & Rajamani, S. (2025) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2025.0104 · Cited by 3 · see citing works
Why is Abiogenesis Such a Tough Nut to Crack?
Abel, D. L. (2024) · Archives of Microbiology & Immunology · doi:10.26502/ami.936500182 · Cited by 3 · see citing works
An Evolutionary Process Without Variation and SelectionPreprint
Gabora, L. M., & Steel, M. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.08.30.274407 · Cited by 2 · see citing works
A Fundamentally New Perspective on the Origin and Evolution of LifePreprint
Liu, S. V. (2008) · arXiv (Cornell University) · doi:10.48550/arxiv.0811.3653 · Cited by 2 · see citing works
Chemical Origins of Life, Agency, and Meaning
Sharov, A. A. (2024) · Wiley eBooks · doi:10.1002/9781119865667.ch9 · Cited by 2 · see citing works
von Meijenfeldt, F. A. B. (2014) · Cited by 1 · see citing works
Evolutionary attributes of simulated prebiotic metabolic networks
Markovitch, O., & Lancet, D. (2011) · European Conference on Artificial Life · doi:10.7551/978-0-262-29714-1-ch076 · Cited by 1 · see citing works
Self-citationChemical Heredity as Group Selection at the Molecular LevelPreprint
Markovitch, O., Witkowski, O., & Virgo, N. (2018) · arXiv (Cornell University) · doi:10.48550/arxiv.1802.08024 · Cited by 1 · see citing works
Researchchiral symmetry breaking in early molecular networks
Kafri, R., Markovitch, O., & Lancet, D. (2010)
Self-citationEvolution, Selection and the Metabolic Foundations of the RNA World.
Pratt, A. J. (2010) · Artificial Life
An Artificial Chemistry for the 'Lipid World' Scenario
Shenhav, B. (2014) · Conference on Artificial Life (ALIFE) · doi:10.1162/978-0-262-32621-6-ch131
Self-citationMolecular Transformation for Self-reproducing Vesicles and Underlying Analysis Methods
Toyota, T., Ohtani, A., & Sugiyama, H. (2021) · Chemical and Pharmaceutical Bulletin · doi:10.1248/cpb.c21-00216
Sharov, A. A., & Tønnessen, M. (2021) · Biosemiotics/Biosemiotics. Bookseries · doi:10.1007/978-3-030-89484-9_5
- Authors
- Shenhav, B., Oz, A., & Lancet, D.
- Affiliations
- Crown Human Genome Center (IL)
- ORCID
- Venue
- Philosophical Transactions of the Royal Society B: Biological Sciences
- Publisher
- The Royal Society
- Published
- 2007-05-09
- Volume
- 362
- Issue
- 1486
- Pages
- 1813-1819
- ISSN
- 0962-8436 (ISSN-L)
- 1471-2970
- PMC
- PMC2442395
- OpenAlex
- W2156623436
- Cited by
- 40
- References
- 31
- Citations by year
- 2025: 1 · 2024: 2 · 2023: 3 · 2021: 3 · 2020: 1 · 2018: 4 · 2017: 1 · 2016: 1 · 2014: 5 · 2013: 2 · 2012: 3
- FWCI
- 2.00
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Philosophical Transactions of the Royal Society B Biological Sciences (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Physical Sciences › Physics and Astronomy › Astronomy and Astrophysics › Origins and Evolution of Life
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Physical Sciences › Computer Science › Computational Theory and Mathematics › Cellular Automata and Applications
- Keywords
- protocells, origin of life, quasi-stationary states, molecular assembly
- MeSH terms
- Cell Physiological Phenomena, Computer Simulation, Environment, Biological Evolution, Models, Biological
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
