Replication of Simulated Prebiotic Amphiphilic Vesicles in a Finite Environment Exhibits Complex Behavior That Includes High Progeny Variability and Competition
Open accessAbstract
We studied the simulated replication and growth of prebiotic vesicles composed of 140 phospholipids and cholesterol using our R-GARD (Real Graded Autocatalysis Replication Domain) formalism that utilizes currently extant lipids that have known rate constants of lipid-vesicle interactions from published experimental data. R-GARD normally modifies kinetic parameters of lipid-vesicle interactions based on vesicle composition and properties. Our original R-GARD model tracked the growth and division of one vesicle at a time in an environment with unlimited lipids at a constant concentration. We explore here a modified model where vesicles compete for a finite supply of lipids. We observed that vesicles exhibit complex behavior including initial fast unrestricted growth, followed by intervesicle competition for diminishing resources, then a second growth burst driven by better-adapted vesicles, and ending with a final steady state. Furthermore, in simulations without kinetic parameter modifications ("invariant kinetics"), the initial replication was an order of magnitude slower, and vesicles' composition variability at the final steady state was much lower. The complex kinetic behavior was not observed either in the previously published R-GARD simulations or in additional simulations presented here with only one lipid component. This demonstrates that both a finite environment (inducing selection) and multiple components (providing variation for selection to act upon) are crucial for portraying evolution-like behavior. Such properties can improve survival in a changing environment by increasing the ability of early protocellular entities to respond to rapid environmental fluctuations likely present during abiogenesis both on Earth and possibly on other planets. This in silico simulation predicts that a relatively simple in vitro chemical system containing only lipid molecules might exhibit properties that are relevant to prebiotic processes. Key Words: Phospholipid vesicles-Prebiotic compartments-Prebiotic vesicle competition-Prebiotic vesicle variability. Astrobiology 18, 419-430.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
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?
GARD is much less abstract than many other models for life's origin because it uses rigorous chemical kinetic equations, and it is the only model in its genre that uses experiment-based graded catalytic parameters and in two papers also the properties of real lipid molecules.
“This is wrong: in using rigorous chemical kinetic equations, GARD is much less abstract than many other models for life's origin. Further, it is the only model in its genre that uses experiment-based graded catalytic parameters (§4) and in two papers also the properties of real lipid molecules [60,119].”
From Systems protobiology: origin of life in lipid catalytic networks (2018) · cites this paper as [119]
Split into 2 atoms — 0 confirmed, 2 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.
Experimental — accuracy not yet measuredIn R-GARD simulations with a finite supply of amphiphiles, complex kinetic behaviour including inter-assembly competition was transiently observed.
“In such simulations, we were able to transiently observe complex kinetic behaviour, including inter-assembly competition.”
From Systems protobiology: origin of life in lipid catalytic networks (2018) · cites this paper as [119]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
The antiquity of RNA-based evolution.
Joyce, G. F. (2002) · Nature · doi:10.1038/418214a · Cited by 1,070 · 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-citationThe Emergence of Competition Between Model Protocells
Chen, I. A., Roberts, R. W., & Szostak, J. W. (2004) · Science · doi:10.1126/science.1100757 · Cited by 435 · see citing works
Compositional 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-citationDamer, B., & Deamer, D. (2015) · Life · doi:10.3390/life5010872 · Cited by 309 · see citing works
Lipid formation by aqueous Fischer-Tropsch-type synthesis over a temperature range of 100 to 400 °C
Rushdi, A. I., & Simoneit, B. R. T. (2001) · Origins of life and evolution of the biosphere · doi:10.1023/a:1006702503954 · Cited by 274 · see citing works
Deamer, D. W., & Pashley, R. M. (1989) · Origins of life and evolution of the biosphere · doi:10.1007/bf01808285 · Cited by 272 · see citing works
Boundary structures are formed by organic-components of the Murchison carbonaceous chondrite
Deamer, D. W. (1985) · Nature · doi:10.1038/317792a0 · Cited by 270 · see citing works
Self-assembling amphiphilic molecules: Synthesis in simulated interstellar/precometary ices
Dworkin, J. P., Deamer, D. W., Sandford, S. A., & Allamandola, L. J. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.98.3.815 · Cited by 244 · see citing works
The origin of the RNA world: Co-evolution of genes and metabolism
Copley, S. D., Smith, E., & Morowitz, H. J. (2007) · Bioorganic Chemistry · doi:10.1016/j.bioorg.2007.08.001 · Cited by 184 · see citing works
Self-reproducing catalyst drives repeated phospholipid synthesis and membrane growth
Hardy, M. D., Yang, J., Selimkhanov, J., Cole, C. M., Tsimring, L. S., & Devaraj, N. K. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1506704112 · Cited by 181 · see citing works
Chain-length heterogeneity allows for the assembly of fatty acid vesicles in dilute solutions
Budin, I., Prywes, N., Zhang, N., & Szostak, J. W. (2014) · Biophysical Journal · doi:10.1016/j.bpj.2014.07.067 · Cited by 88 · 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-citationPeriodic vesicle formation in tectonic fault zones: An ideal scenario for molecular evolution
Mayer, C., Schreiber, U., & Dávila, M. J. (2015) · Origins of Life and Evolution of Biospheres · doi:10.1007/s11084-015-9411-z · Cited by 42 · see citing works
Flagged first, then by citations
Research works printed but not linked: 29
- Adamala K. and Szostak J.W. (2013) Competition between model protocells driven by an encapsulated catalyst. Nat Chem 5: 495– 501 23695631 PMC4041014
- Armstrong D.L., Markovitch O., Zidovetzki R., and Lancet D. (2011) Replication of simulated prebiotic amphiphile vesicles controlled by experimental lipid physicochemical properties. Phys Biol 8, doi: 10.1088/1478-3975/8/6/066001 21946049 · DOI · Paper page
- Blain J.C. and Szostak J.W. (2014) Progress toward synthetic cells. Annu Rev Biochem 83: 615– 640 24606140
- Božič B. and Svetina S. (2004) A relationship between membrane properties forms the basis of a selectivity mechanism for vesicle self-reproduction. Eur Biophys J 33: 565– 571 15095026
- Božič B. and Svetina S. (2007) Vesicle self-reproduction: the involvement of membrane hydraulic and solute permeabilities. Eur Phys J E Soft Matter 24: 79– 90 17882352
- Budin I. and Szostak J.W. (2011) Physical effects underlying the transition from primitive to modern cell membranes. Proc Natl Acad Sci USA 108: 5249– 5254 21402937 PMC3069173
- Cronin J.R. (1998) Clues from the origin of the Solar System: meteorites. In The Molecular Origin of Life: Assembling Pieces of the Puzzle, edited by Andre B., Cambridge University Press, Cambridge, UK, pp 119– 146
- Damer B. (2016) A field trip to the Archaean in search of Darwin's warm little pond. Life (Basel) 6, doi: 10.3390/life6020021 PMC4931458 27231942 · DOI
- Fellermann H. and Solé R.V. (2007) Minimal model of self-replicating nanocells: a physically embodied information-free scenario. Philos Trans R Soc Lond B Biol Sci 362: 1803– 1811 17510020 PMC2442394
- Georgiou C.D. and Deamer D.W. (2014) Lipids as universal biomarkers of extraterrestrial life. Astrobiology 14: 541– 549 24735484
- Hanczyc M.M., Fujikawa S.M., and Szostak J.W. (2003) Experimental models of primitive cellular compartments: encapsulation, growth, and division. Science 302: 618– 622 14576428 PMC4484575
- Hargreaves W.R., Mulvihill S.J., and Deamer D.W. (1977) Synthesis of phophospholipids and membranes in prebiotic conditions. Nature 266: 78– 80 840303
- Mavelli F. and Ruiz-Mirazo K. (2010) ENVIRONMENT: a computational platform to stochastically simulate reacting and self-reproducing lipid compartments. Phys Biol 7, doi: 10.1088/1478-3975/7/3/036002 20702920 · DOI
- McCollom T.M., Ritter G., and Simoneit B.R. (1999) Lipid synthesis under hydrothermal conditions by Fischer-Tropsch-type reactions. Orig Life Evol Biosph 29: 153– 166 10227201
- Patel B.H., Percivalle C., Ritson D.J., Duffy C.D., and Sutherland J.D. (2015) Common origins of RNA, protein and lipid precursors in a cyanosulfidic protometabolism. Nat Chem 7: 301– 307 25803468 PMC4568310
- Pekkonen M., Ketola T., and Laakso J.T. (2013) Resource availability and competition shape the evolution of survival and growth ability in a bacterial community. PLoS One 8, doi: 10.1371/journal.pone.0076471 PMC3787024 24098791 · DOI
- Pohorille A. and Deamer D. (2009) Self-assembly and function of primitive cell membranes. Res Microbiol 160: 449– 456 19580865
- Pulselli R.M., Simoncini E., and Tiezzi E. (2009) Self-organization in dissipative structures: a thermodynamic theory for the emergence of prebiotic cells and their epigenetic evolution. Biosystems 3: 237– 241 19758548
- Regis E. (2009) What is Life? Investigating the Nature of Life in the Age of Synthetic Biology, Oxford University Press, Oxford, UK
- Schrum J.P., Zhu T.F., and Szostak J.W. (2010) The origins of cellular life. Cold Spring Harb Perspect Biol 2, doi: 10.1101/cshperspect.a002212 PMC2926753 20484387 · DOI · Paper page
- Shenhav B., Bar-Even A., Kafri R., and Lancet D. (2005) Polymer GARD: computer simulation of covalent bond formation in reproducing molecular assemblies. Orig Life Evol Biosph 35: 111– 133 16010993
- Shirt-Ediss B., Ruiz-Mirazo K., Mavelli F., and Solé R.V. (2014) Modelling lipid competition dynamics in heterogeneous protocell populations. Sci Rep 4, doi: 10.1038/srep05675 PMC4097352 25024020 · DOI
- Svetina S. (2012) Cellular life could have emerged from properties of vesicles. Orig Life Evol Biosph 42: 483– 486 23073647
- Szostak J.W. (2011) An optimal degree of physical and chemical heterogeneity for the origin of life? Philos Trans R Soc Lond B Biol Sci 366: 2894– 2901 21930580 PMC3158921
- Takakura K., Toyota T., and Sugawara T. (2003) A novel system of self-reproducing giant vesicles. J Am Chem Soc 125: 8134– 8140 12837083
- Takakura K., Toyota T., and Sugawara T. (2004) A novel system of self-reproducing giant vesicles. J Am Chem Soc 125: 8134– 8140 12837083
- Thomas J.A. and Rana F.R. (2007) The influence of environmental conditions, lipid composition, and phase behavior on the origin of cell membranes. Orig Life Evol Biosph 37: 267– 285 17361322
- Toyota T., Takakura K., Kageyama Y., Kurihara K., Maru N., Ohnuma K., Kaneko K., and Sugawara T. (2008) Population study of sizes and components of self-reproducing giant multilamellar vesicles. Langmuir 24: 3037– 3044 18278955
- Zhu T.F. and Szostak J.W. (2009) Coupled growth and division of model protocell membranes. J Am Chem Soc 131: 5705– 5713 19323552 PMC2669828
Cited by
Sorted by citations
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-citation
- Authors
- Armstrong, D. L., Lancet, D., & Zidovetzki, R.
- Affiliations
- University of California, Riverside (US)
- Weizmann Institute of Science (IL)
- Corresponding author
- Zidovetzki, Raphael
- Venue
- Astrobiology
- Publisher
- SAGE Publications
- Published
- 2018-04
- Volume
- 18
- Issue
- 4
- Pages
- 419-430
- ISSN
- 1531-1074 (ISSN-L)
- 1557-8070
- PMC
- PMC5910049
- OpenAlex
- W2795159781
- Cited by
- 13
- References
- 14
- Citations by year
- 2026: 1 · 2025: 1 · 2024: 4 · 2023: 1 · 2021: 2 · 2020: 1 · 2019: 2 · 2018: 1
- FWCI
- 0.80
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Astrobiology (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion, other-oa)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Funders
- Weizmann Institute of Science
- 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
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Keywords
- phospholipid vesicles, protocells, origin of life, selection, computer simulation, cholesterol
- MeSH terms
- Computer Simulation, Environment, Kinetics, Lipids, Models, Chemical, Earth, Planet
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
