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Life from the Edge of Synthetic Biology
Intellect , 309 (2024); https://doi.org/10.1386/9781789387926_16
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References

  1. Bachmann, Pascale Angelica , Walde, Peter , Luisi, Pier Luigi and Lang Jacques (1991), ‘Self-replicating micelles: Aqueous micelles and enzymatically driven reactions in reverse micelles’, Journal of the American Chemical Society, 113:22, pp. 8204–09.
     [Google Scholar]
  2. Bachmann, Pascale Angelica , Luisi, Pier Luigi and Lang, Jacques (1992), ‘Autocatalytic self-replicating micelles as models for prebiotic structures’, Nature, 357, pp. 57–59.
     [Google Scholar]
  3. Bak, Per , Tang, Chao and Wiesenfeld, Kurt (1987), ‘Self-organized criticality: An explanation of the 1/f noise’, Physical Review Letters, 59:4, pp. 381–84.
     [Google Scholar]
  4. Bechtel, William and Bich, Leonardo (2021), ‘Grounding cognition: Heterarchical control mechanisms in biology’, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, 376:1820.
     [Google Scholar]
  5. Bedau, Mark A. and Cleland, Carol E. (2010), The Nature of Life: Classical and Contemporary Perspectives from Philosophy and Science, Cambridge: Cambridge University Press.
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  6. Bedau, Mark A. , Parke , Emily C. , Tangen, Uwe and Hantsche-Tangen, Brigitte (2009), ‘Social and ethical checkpoints for bottom-up synthetic biology, or protocells’, Systems and Synthetic Biology, 3:1, pp. 65–75.
     [Google Scholar]
  7. Benner, Steven A. and Sismour, A. Michael (2005), ‘Synthetic biology’, Nature Reviews Genetics, 6, pp. 533–43.
     [Google Scholar]
  8. Bich, Leonardo and Frick, Ramiro (2018), ‘Synthetic modelling of biological communication: A theoretical and operational framework for the investigation of minimal life and cognition’, Complex Systems, 27:3, pp. 267–87.
     [Google Scholar]
  9. Bich, Leonardo and Green, Sara (2018), ‘Is defining life pointless? Operational definitions at the frontiers of biology’, Synthese, 195:9, pp. 3919–46.
     [Google Scholar]
  10. Bich, Leonardo and Moreno, Alvaro (2016), ‘The role of regulation in the origin and synthetic modelling of minimal cognition’, Biosystems, 148, pp. 12–21.
     [Google Scholar]
  11. Bitbol, Michel and Luisi, Pier Luigi (2004), ‘Autopoiesis with or without cognition: Defining life at its edge’, Journal of the Royal Society Interface, 1:1, pp. 99–107.
     [Google Scholar]
  12. Chiarabelli, Christiano and Luisi, Pier Luigi (2014), ‘Chemical synthetic biology’, Science Progress, 97:1, pp. 48–61.
     [Google Scholar]
  13. Damiano, Luisa and Luisi, Pier Luigi (2010), ‘Towards an autopoietic redefinition of life’, Origins of Life and Evolution of Biospheres, 40:2, pp. 145–49.
     [Google Scholar]
  14. de Souza, Tereza Pereira , Fahr, Alfred , Luisi, Pier Luigi and Stano, Pasquale (2014), ‘Spontaneous encapsulation and concentration of biological macromolecules in liposomes: An intriguing phenomenon and its relevance in origins of life’, Journal of Molecular Evolution, 79:5&6, pp. 179–92.
     [Google Scholar]
  15. de Souza, Tereza Pereira , Stano, Pasquale , Steiniger, Frank , D'Aguanno, Erica , Altamura, Emiliano , Fahr, Alfred and Luisi, Pier Luigi (2012), ‘Encapsulation of ferritin, ribosomes, and ribo-peptide complexes inside liposomes: Insights into the origin of metabolism’, Origins of Life and Evolution of Biospheres, 42:5, pp. 421–28.
     [Google Scholar]
  16. Engels, Friedrich (1933), Dialectics of Nature (in Russian), Moscow: Partizdat.321
    [Google Scholar]
  17. Forster, Anthony C. and Church, George M. (2007), ‘Synthetic biology projects in vitro’, Genome Research, 17, pp. 1–6.
     [Google Scholar]
  18. Gil, Rosario , Silva, Francisco J. , Peretó, Juli and Moya, Andrés (2004), ‘Determination of the core of a minimal bacteria gene set’, Microbiology and Molecular Biology Review, 68:3, pp. 518–37.
     [Google Scholar]
  19. Green, Sara (2022), ‘Philosophy of systems and synthetic biology’, in E. N. Zalta (ed.), The Stanford Encyclopedia of Philosophy, Stanford, CA: The Metaphysics Research Lab, Center for the Study of Language and Information (CSLI), Stanford University (Summer), https://plato.stanford.edu/archives/sum2022/entries/systems-synthetic-biology/. Accessed 31 May 2023 .
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  20. Hays, Lindsey, L. (editor-in-chief) (2015), NASA Astrobiology Strategy. National Aeronautics and Space Administration, Washington, DC: NASA Astrobiology Institute.
     [Google Scholar]
  21. Hine, Robert (ed.) (2019), ‘Systems biology’, in A Dictionary of Biology, 8th ed., New York: Oxford University Press.
     [Google Scholar]
  22. Joyce, Gerald F. (1994), ‘Foreword’, in D. W. Deamer and G. R. Fleischaker (eds), Origins of Life: The Central Concepts, Boston, MA: Jones & Bartlett, pp. xi–xii.
     [Google Scholar]
  23. Luisi, Pier Luigi (1996), Remedius l'alchimista, Firenze: Giunti Editore.
     [Google Scholar]
  24. Luisi, Pier Luigi (1998), About Various Definitions of Life: Origins of Life and Evolution of the Biosphere, 28, pp. 613–22.
     [Google Scholar]
  25. Luisi, Pier Luigi (2016), The Emergence of Life: From Chemical Origins to Synthetic Biology, 2nd ed., Cambridge: Cambridge University Press.
     [Google Scholar]
  26. Luisi, Pier Luigi (2018), ‘The system view of the origin of cellular life’, Archives of Life Science and Nutritional Research, 1:1, pp. 1–10.
     [Google Scholar]
  27. Luisi, Pier Luigi (2020), ‘Why the origin of life is still a mystery?’, Journal of Systems Chemistry, 8, pp. 1–8.
     [Google Scholar]
  28. Luisi, Pier Luigi , Allegretti, Matteo , de Souza, Tereza Pereira , Steiniger, Frank , Fahr, Alfred and Stano, Pasquale (2010), ‘Spontaneous protein overcrowding in liposomes: A new vista for the origin of cellular metabolism’, ChemBioChem, 11:14, pp. 1989–92.
     [Google Scholar]
  29. Luisi, Pier Luigi , Ferri, Francisca and Stano, Pasquale (2006), ‘Approaches to semi-synthetic minimal cells: A review’, Naturwissenschaften, 93:1, pp. 1–13.
     [Google Scholar]
  30. Luisi, Pier Luigi and Stano, Pasquale (eds) (2011), The Minimal Cell: The Biophysics of Cell Compartment and the Origin of Cell Functionality, Dordrecht: Springer.
     [Google Scholar]
  31. Maturana, Humberto R. and Varela, Francisco J. ([1973] 1980), Autopoiesis and Cognition: The Realization of the Living, Dordrecht: D. Reidel Publishing, pp. 59–145.
     [Google Scholar]
  32. Maturana, Humberto R. ([1987] 1992), The Tree of Knowledge: The Biological Roots of Human Understanding, Revised Edition, Boulder, CO: Shambhala Publications.
     [Google Scholar]
  33. Murtas, Giovanni , Kuruma, Yutetsu , Bianchini, Paolo , Diaspro, Alberto and Luisi, Pier Luigi (2007), ‘Protein synthesis in liposomes with a minimal set of enzymes’, Biochemical and Biophysical Research Commununications, 363:1, pp. 12–17.322
    [Google Scholar]
  34. Oberholzer, Thomas , Wick, Roger , Luisi, Pier Luigi and Biebricher, Christof K. (1995), ‘Enzymatic RNA replication in self-reproducing vesicles: An approach to a minimal cell’, Biochemical and Biophysical Research Commununications, 207, pp. 250–59.
     [Google Scholar]
  35. Oparin, Aleksandr Ivanovich ([1938] 1965), The Origin of Life, 2nd ed. (trans. S. Morgulis), New York: Dover Publications, Inc. [First published in Russian as Vozniknovenie zhizni na zemle, Moscow: Izd. Akad. Nauk SSSR, 1936].
     [Google Scholar]
  36. Pfeifer, Blaine A. , Admiraal, Suzanne J. , Gramajo, Hugo , Cane, David E. and Khosla, Chaitan (2001), ‘Biosynthesis of complex polyketides in a metabolically engineered strain of E. coli’, Science, 291:5509, pp. 1790–92.
     [Google Scholar]
  37. Ruiz-Mirazo, Kepa , Peretó, Juli and Moreno, Alvaro (2004), ‘A universal definition of life: Autonomy and open-ended evolution’, Origins of Life and Evolution of the Biosphere, 34:3, pp. 323–46.
     [Google Scholar]
  38. Schmidli, Peter Kurt , Schurtenberger, Peter and Luisi, Pier Luigi (1991), ‘Liposome-mediated enzymatic synthesis of phosphatidylcholine as an approach to self-replicating liposomes’, Journal of the American Chemical Society, 113:21, pp. 8127–30.
     [Google Scholar]
  39. Stano, Pasquale , Carrara, Paolo , Kuruma, Yutetsu , de Souza, Tereza Pereira and Luisi, Pier Luigi (2011), ‘Compartmentalized reactions as a case of soft-matter biotechnology: Synthesis of proteins and nucleic acids inside lipid vesicles’, Journal of Materials Chemistry, 21, pp. 18887–902.
     [Google Scholar]
  40. Stano, Pasquale , de Souza, Tereza Pereira , Carrara, Paolo , Altamura, Emiliano , D'Aguanno, Erica , Caputo, Margherita , Luisi, Pier Luigi and Mavelli, Fabio (2015), ‘Recent biophysical issues about the preparation of solute-filled lipid vesicles’, Mechanics of Advanced Materials and Structures, 22:9, pp. 748–59.
     [Google Scholar]
  41. Van Duijn, Marc , Keijzer, Fred and Franken, Daan (2006), ‘Principles of minimal cognition: Casting cognition as sensorimotor coordination’, Adaptive Behavior, 14:2, pp. 157–70.
     [Google Scholar]
  42. Varela, Francisco J. (2000), El Fenómeno de la Vida, Santiago de Chile: Dolmen Ediciones.
     [Google Scholar]
  43. Varela, Francisco J. , Maturana, Humberto R. and Uribe, Ricardo B. (1974), ‘Autopoiesis: The organization of living system, its characterization and a model’, Biosystems, 5:4, pp. 187–96.
     [Google Scholar]
  44. Walde, Peter , Wick, Roger , Fresta, Massimo , Mangone, Annarosa and Luisi, Pier Luigi (1994), ‘Autopoietic self-reproduction of fatty acid vesicles’, Journal of the American Chemical Society, 116:26, pp. 11649–54.
     [Google Scholar]

References

  1. Bachmann, Pascale Angelica , Walde, Peter , Luisi, Pier Luigi and Lang Jacques (1991), ‘Self-replicating micelles: Aqueous micelles and enzymatically driven reactions in reverse micelles’, Journal of the American Chemical Society, 113:22, pp. 8204–09.
     [Google Scholar]
  2. Bachmann, Pascale Angelica , Luisi, Pier Luigi and Lang, Jacques (1992), ‘Autocatalytic self-replicating micelles as models for prebiotic structures’, Nature, 357, pp. 57–59.
     [Google Scholar]
  3. Bak, Per , Tang, Chao and Wiesenfeld, Kurt (1987), ‘Self-organized criticality: An explanation of the 1/f noise’, Physical Review Letters, 59:4, pp. 381–84.
     [Google Scholar]
  4. Bechtel, William and Bich, Leonardo (2021), ‘Grounding cognition: Heterarchical control mechanisms in biology’, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, 376:1820.
     [Google Scholar]
  5. Bedau, Mark A. and Cleland, Carol E. (2010), The Nature of Life: Classical and Contemporary Perspectives from Philosophy and Science, Cambridge: Cambridge University Press.
     [Google Scholar]
  6. Bedau, Mark A. , Parke , Emily C. , Tangen, Uwe and Hantsche-Tangen, Brigitte (2009), ‘Social and ethical checkpoints for bottom-up synthetic biology, or protocells’, Systems and Synthetic Biology, 3:1, pp. 65–75.
     [Google Scholar]
  7. Benner, Steven A. and Sismour, A. Michael (2005), ‘Synthetic biology’, Nature Reviews Genetics, 6, pp. 533–43.
     [Google Scholar]
  8. Bich, Leonardo and Frick, Ramiro (2018), ‘Synthetic modelling of biological communication: A theoretical and operational framework for the investigation of minimal life and cognition’, Complex Systems, 27:3, pp. 267–87.
     [Google Scholar]
  9. Bich, Leonardo and Green, Sara (2018), ‘Is defining life pointless? Operational definitions at the frontiers of biology’, Synthese, 195:9, pp. 3919–46.
     [Google Scholar]
  10. Bich, Leonardo and Moreno, Alvaro (2016), ‘The role of regulation in the origin and synthetic modelling of minimal cognition’, Biosystems, 148, pp. 12–21.
     [Google Scholar]
  11. Bitbol, Michel and Luisi, Pier Luigi (2004), ‘Autopoiesis with or without cognition: Defining life at its edge’, Journal of the Royal Society Interface, 1:1, pp. 99–107.
     [Google Scholar]
  12. Chiarabelli, Christiano and Luisi, Pier Luigi (2014), ‘Chemical synthetic biology’, Science Progress, 97:1, pp. 48–61.
     [Google Scholar]
  13. Damiano, Luisa and Luisi, Pier Luigi (2010), ‘Towards an autopoietic redefinition of life’, Origins of Life and Evolution of Biospheres, 40:2, pp. 145–49.
     [Google Scholar]
  14. de Souza, Tereza Pereira , Fahr, Alfred , Luisi, Pier Luigi and Stano, Pasquale (2014), ‘Spontaneous encapsulation and concentration of biological macromolecules in liposomes: An intriguing phenomenon and its relevance in origins of life’, Journal of Molecular Evolution, 79:5&6, pp. 179–92.
     [Google Scholar]
  15. de Souza, Tereza Pereira , Stano, Pasquale , Steiniger, Frank , D'Aguanno, Erica , Altamura, Emiliano , Fahr, Alfred and Luisi, Pier Luigi (2012), ‘Encapsulation of ferritin, ribosomes, and ribo-peptide complexes inside liposomes: Insights into the origin of metabolism’, Origins of Life and Evolution of Biospheres, 42:5, pp. 421–28.
     [Google Scholar]
  16. Engels, Friedrich (1933), Dialectics of Nature (in Russian), Moscow: Partizdat.321
    [Google Scholar]
  17. Forster, Anthony C. and Church, George M. (2007), ‘Synthetic biology projects in vitro’, Genome Research, 17, pp. 1–6.
     [Google Scholar]
  18. Gil, Rosario , Silva, Francisco J. , Peretó, Juli and Moya, Andrés (2004), ‘Determination of the core of a minimal bacteria gene set’, Microbiology and Molecular Biology Review, 68:3, pp. 518–37.
     [Google Scholar]
  19. Green, Sara (2022), ‘Philosophy of systems and synthetic biology’, in E. N. Zalta (ed.), The Stanford Encyclopedia of Philosophy, Stanford, CA: The Metaphysics Research Lab, Center for the Study of Language and Information (CSLI), Stanford University (Summer), https://plato.stanford.edu/archives/sum2022/entries/systems-synthetic-biology/. Accessed 31 May 2023 .
     [Google Scholar]
  20. Hays, Lindsey, L. (editor-in-chief) (2015), NASA Astrobiology Strategy. National Aeronautics and Space Administration, Washington, DC: NASA Astrobiology Institute.
     [Google Scholar]
  21. Hine, Robert (ed.) (2019), ‘Systems biology’, in A Dictionary of Biology, 8th ed., New York: Oxford University Press.
     [Google Scholar]
  22. Joyce, Gerald F. (1994), ‘Foreword’, in D. W. Deamer and G. R. Fleischaker (eds), Origins of Life: The Central Concepts, Boston, MA: Jones & Bartlett, pp. xi–xii.
     [Google Scholar]
  23. Luisi, Pier Luigi (1996), Remedius l'alchimista, Firenze: Giunti Editore.
     [Google Scholar]
  24. Luisi, Pier Luigi (1998), About Various Definitions of Life: Origins of Life and Evolution of the Biosphere, 28, pp. 613–22.
     [Google Scholar]
  25. Luisi, Pier Luigi (2016), The Emergence of Life: From Chemical Origins to Synthetic Biology, 2nd ed., Cambridge: Cambridge University Press.
     [Google Scholar]
  26. Luisi, Pier Luigi (2018), ‘The system view of the origin of cellular life’, Archives of Life Science and Nutritional Research, 1:1, pp. 1–10.
     [Google Scholar]
  27. Luisi, Pier Luigi (2020), ‘Why the origin of life is still a mystery?’, Journal of Systems Chemistry, 8, pp. 1–8.
     [Google Scholar]
  28. Luisi, Pier Luigi , Allegretti, Matteo , de Souza, Tereza Pereira , Steiniger, Frank , Fahr, Alfred and Stano, Pasquale (2010), ‘Spontaneous protein overcrowding in liposomes: A new vista for the origin of cellular metabolism’, ChemBioChem, 11:14, pp. 1989–92.
     [Google Scholar]
  29. Luisi, Pier Luigi , Ferri, Francisca and Stano, Pasquale (2006), ‘Approaches to semi-synthetic minimal cells: A review’, Naturwissenschaften, 93:1, pp. 1–13.
     [Google Scholar]
  30. Luisi, Pier Luigi and Stano, Pasquale (eds) (2011), The Minimal Cell: The Biophysics of Cell Compartment and the Origin of Cell Functionality, Dordrecht: Springer.
     [Google Scholar]
  31. Maturana, Humberto R. and Varela, Francisco J. ([1973] 1980), Autopoiesis and Cognition: The Realization of the Living, Dordrecht: D. Reidel Publishing, pp. 59–145.
     [Google Scholar]
  32. Maturana, Humberto R. ([1987] 1992), The Tree of Knowledge: The Biological Roots of Human Understanding, Revised Edition, Boulder, CO: Shambhala Publications.
     [Google Scholar]
  33. Murtas, Giovanni , Kuruma, Yutetsu , Bianchini, Paolo , Diaspro, Alberto and Luisi, Pier Luigi (2007), ‘Protein synthesis in liposomes with a minimal set of enzymes’, Biochemical and Biophysical Research Commununications, 363:1, pp. 12–17.322
    [Google Scholar]
  34. Oberholzer, Thomas , Wick, Roger , Luisi, Pier Luigi and Biebricher, Christof K. (1995), ‘Enzymatic RNA replication in self-reproducing vesicles: An approach to a minimal cell’, Biochemical and Biophysical Research Commununications, 207, pp. 250–59.
     [Google Scholar]
  35. Oparin, Aleksandr Ivanovich ([1938] 1965), The Origin of Life, 2nd ed. (trans. S. Morgulis), New York: Dover Publications, Inc. [First published in Russian as Vozniknovenie zhizni na zemle, Moscow: Izd. Akad. Nauk SSSR, 1936].
     [Google Scholar]
  36. Pfeifer, Blaine A. , Admiraal, Suzanne J. , Gramajo, Hugo , Cane, David E. and Khosla, Chaitan (2001), ‘Biosynthesis of complex polyketides in a metabolically engineered strain of E. coli’, Science, 291:5509, pp. 1790–92.
     [Google Scholar]
  37. Ruiz-Mirazo, Kepa , Peretó, Juli and Moreno, Alvaro (2004), ‘A universal definition of life: Autonomy and open-ended evolution’, Origins of Life and Evolution of the Biosphere, 34:3, pp. 323–46.
     [Google Scholar]
  38. Schmidli, Peter Kurt , Schurtenberger, Peter and Luisi, Pier Luigi (1991), ‘Liposome-mediated enzymatic synthesis of phosphatidylcholine as an approach to self-replicating liposomes’, Journal of the American Chemical Society, 113:21, pp. 8127–30.
     [Google Scholar]
  39. Stano, Pasquale , Carrara, Paolo , Kuruma, Yutetsu , de Souza, Tereza Pereira and Luisi, Pier Luigi (2011), ‘Compartmentalized reactions as a case of soft-matter biotechnology: Synthesis of proteins and nucleic acids inside lipid vesicles’, Journal of Materials Chemistry, 21, pp. 18887–902.
     [Google Scholar]
  40. Stano, Pasquale , de Souza, Tereza Pereira , Carrara, Paolo , Altamura, Emiliano , D'Aguanno, Erica , Caputo, Margherita , Luisi, Pier Luigi and Mavelli, Fabio (2015), ‘Recent biophysical issues about the preparation of solute-filled lipid vesicles’, Mechanics of Advanced Materials and Structures, 22:9, pp. 748–59.
     [Google Scholar]
  41. Van Duijn, Marc , Keijzer, Fred and Franken, Daan (2006), ‘Principles of minimal cognition: Casting cognition as sensorimotor coordination’, Adaptive Behavior, 14:2, pp. 157–70.
     [Google Scholar]
  42. Varela, Francisco J. (2000), El Fenómeno de la Vida, Santiago de Chile: Dolmen Ediciones.
     [Google Scholar]
  43. Varela, Francisco J. , Maturana, Humberto R. and Uribe, Ricardo B. (1974), ‘Autopoiesis: The organization of living system, its characterization and a model’, Biosystems, 5:4, pp. 187–96.
     [Google Scholar]
  44. Walde, Peter , Wick, Roger , Fresta, Massimo , Mangone, Annarosa and Luisi, Pier Luigi (1994), ‘Autopoietic self-reproduction of fatty acid vesicles’, Journal of the American Chemical Society, 116:26, pp. 11649–54.
     [Google Scholar]

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