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Antoine Danchin
University of Hong Kong
  1.  97
    Omnipresent Maxwell’s Demons Orchestrate Information Management in Living Cells.Antoine Danchin Gregory Boel, Olivier Danot, Victor de Lorenzo & Antoine Danchin - 2019 - Microbial Biotechnology 12 (2):210-242.
    The development of synthetic biology calls for accurate understanding of the critical functions that allow construction and operation of a living cell. Besides coding for ubiquitous structures, minimal genomes encode a wealth of functions that dissipate energy in an unanticipated way. Analysis of these functions shows that they are meant to manage information under conditions when discrimination of substrates in a noisy background is preferred over a simple recognition process. We show here that many of these functions, including transporters and (...)
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  2.  50
    No Wisdom in the Crowd: Genome Annotation at the Time of Big Data - Current Status and Future Prospects.Antoine Danchin - 2018 - Microbial Biotechnology 11 (4):588-605.
    Science and engineering rely on the accumulation and dissemination of knowledge to make discoveries and create new designs. Discovery-driven genome research rests on knowledge passed on via gene annotations. In response to the deluge of sequencing big data, standard annotation practice employs automated procedures that rely on majority rules. We argue this hinders progress through the generation and propagation of errors, leading investigators into blind alleys. More subtly, this inductive process discourages the discovery of novelty, which remains essential in biological (...)
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  3. Life’s Demons: Information and Order in Biology.Philippe M. Binder & Antoine Danchin - 2011 - EMBO Reports 12 (6):495-499.
    Two decades ago, Rolf Landauer (1991) argued that “information is physical” and ought to have a role in the scientific analysis of reality comparable to that of matter, energy, space and time. This would also help to bridge the gap between biology and mathematics and physics. Although it can be argued that we are living in the ‘golden age’ of biology, both because of the great challenges posed by medicine and the environment and the significant advances that have been made—especially (...)
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  4. A Theory of the Epigenesis of Neuronal Networks by Selective Stabilization of Synapses.Jean Pierre Changeux, Philippe Courrège & Antoine Danchin - 1973 - Proceedings of the National Academy of Sciences Usa 70 (10):2974-8.
    A formalism is introduced to represent the connective organization of an evolving neuronal network and the effects of environment on this organization by stabilization or degeneration of labile synapses associated with functioning. Learning, or the acquisition of an associative property, is related to a characteristic variability of the connective organization: the interaction of the environment with the genetic program is printed as a particular pattern of such organization through neuronal functioning. An application of the theory to the development of the (...)
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  5. Information of the Chassis and Information of the Program in Synthetic Cells.Antoine Danchin - 2009 - Systems and Synthetic Biology 3:125-134.
    Synthetic biology aims at reconstructing life to put to the test the limits of our understanding. It is based on premises similar to those which permitted invention of computers, where a machine, which reproduces over time, runs a program, which replicates. The underlying heuristics explored here is that an authentic category of reality, information, must be coupled with the standard categories, matter, energy, space and time to account for what life is. The use of this still elusive category permits us (...)
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  6. Antifragility and Tinkering in Biology (and in Business) Flexibility Provides an Efficient Epigenetic Way to Manage Risk.Antoine Danchin, Philippe M. Binder & Stanislas Noria - 2011 - Genes 2 (4):998-1016.
    The notion of antifragility, an attribute of systems that makes them thrive under variable conditions, has recently been proposed by Nassim Taleb in a business context. This idea requires the ability of such systems to ‘tinker’, i.e., to creatively respond to changes in their environment. A fairly obvious example of this is natural selection-driven evolution. In this ubiquitous process, an original entity, challenged by an ever-changing environment, creates variants that evolve into novel entities. Analyzing functions that are essential during stationary-state (...)
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  7.  64
    FRUSTRATION: PHYSICO-CHEMICAL PREREQUISITES FOR THE CONSTRUCTION OF A SYNTHETIC CELL.Antoine Danchin & Agnieszka Sekowska - 2008 - In Martin G. Hicks and Carsten Kettner (ed.), Proceedings of the International Beilstein Symposium on Systems Chemistry May 26th – 30th, 2008 Bozen, Italy. Beilstein Institute. pp. 1-19.
    To construct a synthetic cell we need to understand the rules that permit life. A central idea in modern biology is that in addition to the four entities making reality, matter, energy, space and time, a fifth one, information, plays a central role. As a consequence of this central importance of the management of information, the bacterial cell is organised as a Turing machine, where the machine, with its compartments defining an inside and an outside and its metabolism, reads and (...)
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  8.  58
    Les organismes vivants comme pièges à information.Antoine Danchin - 2008 - Ludus Vitalis 16 (30):211-212.
    Life can be defined as combining two entities that rest on completely different physico-chemical properties and on a particular way of handling information. The cell, first, is a « machine », that combines elements which are quite similar (although in a fairly fuzzy way) to those involved in a man-made factory. The machine combines two processes. First, it requires explicit compartmentalisation, including scaffolding structures similar to that of the châssis of engineered machines. In addition, cells define clearly an inside, the (...)
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  9.  58
    Motivated Research.Antoine Danchin - 2010 - EMBO Reports 11 (7):488.
    The dichotomy between the research to generate knowledge and the application of that knowledge to benefit mankind seems to be a recent development. In fact, more than 100 years ago Louis Pasteur avoided this debate altogether: one of his major, yet forgotten, contributions to science was the insight that research and its applications are not opposed, but orthogonal to each other (Stokes, 1997). If Niels Bohr ‘invented’ basic academic research—which was nevertheless the basis for many technological inventions and industrial applications—Pasteur (...)
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