•  62
    COVID-19 Adaptive Humoral Immunity Models: Weakly Neutralizing Versus Antibody-Disease Enhancement Scenarios
    with Ghozlane Yahiaoui, Gabriel Turinici, and Oriane Pagani-Azizi
    Acta Biotheoretica 70 (4): 23. 2022.
    The interplay between the virus, infected cells and immune responses to SARS-CoV-2 is still under debate. By extending the basic model of viral dynamics, we propose here a formal approach to describe neutralisation versus weak (or non-)neutralisation scenarios and compare them with the possible effects of antibody-dependent enhancement (ADE). The theoretical model is consistent with the data available in the literature; we show that both weakly neutralising antibodies and ADE can result in final…Read more
  •  133
    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 proce…Read more
  •  258
    Omnipresent Maxwell’s demons orchestrate information management in living cells
    with Gregory Boel, Olivier Danot, Victor de Lorenzo, Antoine Danchin
    Microbial Biotechnology 12 (2): 210-242. 2019.
    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…Read more
  •  18
    Cells need safety valves
    Bioessays 31 (7): 769-773. 2009.
    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 woul…Read more
  •  16
    The Delphic Boat. What genomes tell us.
    Harvard University Press. 2002.
    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.
  •  20
    Persistent biases in the amino acid composition of prokaryotic proteins
    with Géraldine Pascal and Claudine Médigue
    Bioessays 28 (7): 726-738. 2006.
    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 conte…Read more
  •  317
    A theory of the epigenesis of neuronal networks by selective stabilization of synapses
    with Jean Pierre Changeux and Philippe Courrège
    Proceedings of the National Academy of Sciences Usa 70 (10): 2974-8. 1973.
    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 fun…Read more
  •  109
    Motivated research
    EMBO Reports 11 (7): 488. 2010.
    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 technologic…Read more
  •  5
    Comment peut-on parler de l'automate cérébral aujourd'hui ?
    Revue Philosophique de la France Et de l'Etranger 170 (3). 1980.
    It is perhaps in the functioning of the brain that we can make contextual information most prominent. Indeed, while von Neumann and others invented computers with mimicking the brain in mind, the brain does not appear to behave as a Turing Machine. Neither is it a mechanical automaton. There is no “gost in the machine”. However, nobody would doubt that brain manages information, and in a very efficient way. To my view this is a strong indication that the information we describe when considering …Read more
  •  298
    The logic of metabolism and its fuzzy consequences
    Environmental Microbiology 16 (1): 19-28. 2014.
    Intermediary metabolism molecules are orchestrated into logical pathways stemming from history (L-amino acids, D-sugars) and dynamic constraints (hydrolysis of pyrophosphate or amide groups is the driving force of anabolism). Beside essential metabolites, numerous variants derive from programmed or accidental changes. Broken down, variants enter standard pathways, producing further variants. Macromolecule modification alters enzyme reactions specificity. Metabolism conform thermodynamic laws, pr…Read more
  •  519
    Life’s demons: information and order in biology
    with Philippe M. Binder
    EMBO Reports 12 (6): 495-499. 2011.
    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 in genetics…Read more
  •  257
    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 entiti…Read more
  •  8
    Order and Necessity (edited book)
    Elsevier Sciences Publishers. 1987.
    Because this lecture was a tribute to the contribution of Monod to science it focused on his views, without discussing the work of others who contributed to his achievements. In particular, because Monod was implicitly a platonician/pythagorean (with his emphasis on the importance of beauty in things), he thought that symmetry had to be introduced in the concept of allostery. In fact this was an extra feature that was absent from the original work of Jean-Pierre Changeux on the enzyme threonine …Read more
  •  106
    Les organismes vivants comme pièges à information
    Ludus Vitalis 16 (30): 211-212. 2008.
    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, …Read more
  •  23
    Confidence, tolerance, and allowance in biological engineering: The nuts and bolts of living things
    with Manuel Porcar and Víctor de Lorenzo
    Bioessays 37 (1): 95-102. 2015.
    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 biolog…Read more
  •  182
    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 expresses the …Read more
  •  27
    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-depen…Read more
  •  11
    Une approche biologique de la genèse de l'identité individuelle. Pour introduire notre discours biologique au niveau anthropologique, nous ferons le line entre un exposé purement ethnologique et un exposé d'analyse linguistique. Cette insertion est d'autant plus cruciale qu'il s'agit de présenter ici une approche de l'identité perpendiculaire à l'analyse structurale - comme le temps est orthogonal à l'espace. Plutôt donc que d'entrer immédiatement dans le vif du sujet, je vais user d'un langage …Read more
  •  35
    Permanence and Change
    with Carl R. Lovitt
    Substance 12 (3): 61. 1983.
    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 underli…Read more
  •  21
    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…Read more
  •  282
    Information of the chassis and information of the program in synthetic cells
    Systems and Synthetic Biology 3 125-134. 2009.
    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 pe…Read more