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Antoine Danchin
University of Hong Kong
  1.  25
    "A Critical Note on the Use of the Term" Phenocopy.".Antoine Danchin - 1980 - In Massimo Piattelli-Palmarini (ed.), Language and Learning: The Debate Between Jean Piaget and Noam Chomsky. Harvard University Press.
    The discovery of the concrete basis for genes, and especially the clarification of mechanisms regulating gene expressions (in particular those that bear on the stepwise processing of hereditary information from the sequences of DNA nucleotides to the proteins) was to give flesh to the concept of a genetic program, for these regulations introduce relationships of order between the various elements of information contained in the genes. These order relations are then revealed during the time-dependent expression of the genetic program. They (...)
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  2. 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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  3.  14
    The Delphic Boat. What Genomes Tell Us.Antoine Danchin - 2002 - Harvard University Press.
    Danchin argues that if scientists can reach a level of understanding of genomes, they will be able to resolve the major biological puzzle of the 21st century: the enigma of the living machine that creates the living machine.
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  4. 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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  5. 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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  6.  19
    Confidence, Tolerance, and Allowance in Biological Engineering: The Nuts and Bolts of Living Things.Manuel Porcar, Antoine Danchin & Víctor de Lorenzo - 2015 - Bioessays 37 (1):95-102.
    The emphasis of systems and synthetic biology on quantitative understanding of biological objects and their eventual re-design has raised the question of whether description and construction standards that are commonplace in electric and mechanical engineering are applicable to live systems. The tuning of genetic devices to deliver a given activity is generally context-dependent, thereby undermining the re-usability of parts, and predictability of function, necessary for manufacturing new biological objects. Tolerance and allowance are key aspects of standardization that need to be (...)
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  7. 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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  8. 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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  9.  20
    Persistent Biases in the Amino Acid Composition of Prokaryotic Proteins.Géraldine Pascal, Claudine Médigue & Antoine Danchin - 2006 - Bioessays 28 (7):726-738.
    Correspondence analysis of 28 proteomes selected to span the entire realm of prokaryotes revealed universal biases in the proteins’ amino acid distribution. Integral Inner Membrane Proteins always form an individual cluster, which can then be used to predict protein localisation in unknown proteomes, independently of the organism’s biotope or kingdom. Orphan proteins are consistently rich in aromatic residues. Another bias is also ubiquitous: the amino acid composition is driven by the GþC content of the first codon position. An unexpected bias (...)
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  10.  16
    Cells Need Safety Valves.Antoine Danchin - 2009 - Bioessays 31 (7):769-773.
    In Escherichia coli, the role of lacA, the third gene of the lactose operon, has remained an enigma. I suggest that its role is the consequence of the need for cells to have safety valves that protect them from the osmotic effect created by their permeases. Safety valves allow them to cope with the buildup of osmotic pressure under accidental transient conditions. Multidrug resistance (MDR) efflux, thus named because of our anthropocentrism, is ubiquitous. Yet, the formation of simple leaks would (...)
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  11. 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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  12.  91
    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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  13.  20
    Archives or Palimpsests? Bacterial Genomes Unveil a Scenario for the Origin of Life.Antoine Danchin - 2007 - Biological Theory 2 (1):52-61.
    The three processes needed to create life, compartmentalization, metabolism, and information transfer (memory stored in nucleic acids and manipulation operated by proteins) are embedded in organized genome features. The core of life puts together growth and maintenance (which drives survival), while life in context explores and exploits specific niches. Analysis of gene persistence in a large number of genomes shows that the former constitutes the paleome, which recapitulates the three phases of the origin of life: metabolism of small molecules on (...)
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  14.  83
    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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  15. 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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  16.  35
    Permanence and Change.Antoine Danchin & Carl R. Lovitt - 1983 - Substance 12 (3):61.
    Determinism/indeterminism, permanence /change, global/local — these have been the occasion for disputes that have persisted for ages. Combined in every conceivable fashion, these three pairs have given rise to theories of reality which, though incompatible, nevertheless possess some degree of adequacy. Accounting for the properties of the inorganic world, on invariably confronts several opposing attitudes, each of which questions the pertinence of the continuous/discontinuous pair, which underlies any discussion of the three pairs noted above. Thinkers of Antiquity sought to deal (...)
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