alias bioputing—has been explored for decades. These materials include DNA, RNA and proteins, while the processes include transcription, translation, signal transduction and regulation. Recently, the use of bacteria themselves as living computers has been explored but this use generally falls within the classical paradigm of computing. Computer scientists, however, have a variety of problems to which they seek solutions, while microbiologists are having new insights into the problems bacteria are solving and how they are solving them. Here, we envisage that bacteria might be used for new sorts of computing. These could be based on the capacity of bacteria to grow, move and adapt to a myriad different fickle environments both as individuals and as populations of bacteria plus bacteriophage. New principles might be based on the way that bacteria explore phenotype space via hyperstructure dynamics and the fundamental nature of the cell cycle. This computing might even extend to developing a high level language appropriate to using populations of bacteria and bacteriophage. Here, we offer a speculative tour of what we term bactoputing, namely the use of the natural behaviour of bacteria for calculating." />
Computing with bacterial constituents, cells and populations: from bioputing to bactoputing
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  • 作者：Vic Norris (1) (2)
    Abdallah Zemirline (1) (3)
    Patrick Amar (1) (4)
    Jean Nicolas Audinot (5)
    Pascal Ballet (1) (3)
    Eshel Ben-Jacob (6)
    Gilles Bernot (1) (7)
    Guillaume Beslon (1) (8)
    Armelle Cabin (1) (2)
    Eric Fanchon (1) (9)
    Jean-Louis Giavitto (1) (10)
    Nicolas Glade (1) (9)
    Patrick Greussay (1) (11)
    Yohann Grondin (1) (2)
    James A. Foster (12)
    Guillaume Hutzler (1) (10)
    Jürgen Jost (16) (17)
    Francois Kepes (1)
    Olivier Michel (1) (13)
    Franck Molina (1) (14)
    Jacqueline Signorini (1) (11)
    Pasquale Stano (15)
    Alain R. Thierry (1) (14)
  • 关键词：Biological computing ; Bacteria ; Minimal cell ; Synthetic biology ; Turing ; Origin of life ; Computer science
  • 刊名：Theory in Biosciences
  • 出版年：2011
  • 出版时间：September 2011
  • 年：2011
  • 卷：130
  • 期：3
  • 页码：211-228
  • 全文大小：374KB
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  • 作者单位：Vic Norris (1) (2)
    Abdallah Zemirline (1) (3)
    Patrick Amar (1) (4)
    Jean Nicolas Audinot (5)
    Pascal Ballet (1) (3)
    Eshel Ben-Jacob (6)
    Gilles Bernot (1) (7)
    Guillaume Beslon (1) (8)
    Armelle Cabin (1) (2)
    Eric Fanchon (1) (9)
    Jean-Louis Giavitto (1) (10)
    Nicolas Glade (1) (9)
    Patrick Greussay (1) (11)
    Yohann Grondin (1) (2)
    James A. Foster (12)
    Guillaume Hutzler (1) (10)
    Jürgen Jost (16) (17)
    Francois Kepes (1)
    Olivier Michel (1) (13)
    Franck Molina (1) (14)
    Jacqueline Signorini (1) (11)
    Pasquale Stano (15)
    Alain R. Thierry (1) (14)

    1. Epigenomics Project, Genopole Campus 1, Bat. Genavenir 6, 5 rue Henri Desbruères, 91030, évry Cedex, France
    2. Assemblages Moleculaires: Modelisation et Imagerie SIMS, EA 3829, Faculty of Science, University of Rouen, 76821, Mont-Saint-Aignan, France
    3. LISyC, EA3883, UBO, 20 avenue Le Gorgeu C.S. 93837 BP 809, 29238, Brest Cedex 3, France
    4. Laboratoire de Recherches en Informatique, University of Paris 11 & CNRS UMR 8623, 15 avenue George Clémenceau, 91405, Orsay Cedex, France
    5. Département Science et Analyse des Matériaux, Centre de Recherche Public-Gabriel Lippmann, 4422, Belvaux, Luxembourg
    6. School of Physics and Astronomy, Tel Aviv University, 69978, Tel Aviv, Israel
    7. Laboratoire I3S, Algorithmes-Euclide-B, University of Nice-Sophia Antipolis, 06903, Sophia Antipolis Cedex, France
    8. Computer Sciences Department, Institut National des Sciences Appliquées de Lyon, Batiment Blaise Pascal, 69621, Villeurbanne Cedex, France
    9. Laboratoire TIMC-IMAG, Faculty of Médecine, 38706, La Tronche, France
    10. Laboratory IBISC-LIS project, CNRS FRE 2873, University of Evry-Val d’Essonne, France Université de Paris XII, évry, France
    11. Advanced Computing Laboratory of Saint-Denis, University Paris 8, 93526, Saint-Denis, France
    12. Department of Biological Sciences, University of Idaho, Moscow, ID, 83844-3051, USA
    16. Max Planck Institute for Mathematics in the Sciences, Inselstr.22, 04103, Leipzig, Germany
    17. Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM, 87501, USA
    13. Lab. LACL-Bat P2-40, Faculté des sciences et technologies, 61 Av. du Général de Gaulle, 94010, Créteil Cedex, France
    14. Sysdiag UMR 3145-CNRS/BIO-RAD, Cap Delta 1682 Rue de la Valsiere, 34184, Montpellier Cedex 4, France
    15. Enrico Fermi Research Centre, Compendio del Viminale, 00184, Rome, Italy
文摘
The relevance of biological materials and processes to computing-em class="a-plus-plus">alias bioputing—has been explored for decades. These materials include DNA, RNA and proteins, while the processes include transcription, translation, signal transduction and regulation. Recently, the use of bacteria themselves as living computers has been explored but this use generally falls within the classical paradigm of computing. Computer scientists, however, have a variety of problems to which they seek solutions, while microbiologists are having new insights into the problems bacteria are solving and how they are solving them. Here, we envisage that bacteria might be used for new sorts of computing. These could be based on the capacity of bacteria to grow, move and adapt to a myriad different fickle environments both as individuals and as populations of bacteria plus bacteriophage. New principles might be based on the way that bacteria explore phenotype space via hyperstructure dynamics and the fundamental nature of the cell cycle. This computing might even extend to developing a high level language appropriate to using populations of bacteria and bacteriophage. Here, we offer a speculative tour of what we term bactoputing, namely the use of the natural behaviour of bacteria for calculating.

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