Antoine Danchin

Anticiper les épidémies est le souhait le plus vif de toutes les institutions qui veillent sur la santé publique. Un raisonnement naïf permet de penser qu’il suffit de faire évoluer en laboratoire un organisme potentiellement pathogène pour savoir comment sa descendance pourra devenir plus virulente pour l’homme. Il est alors facile de faire croître cet organisme sur des cellules humaines, qu’il infecte mal pour commencer, puis de retenir ses descendants au fur et à mesure qu’ils deviennent plus infectieux. La vision optimiste affirme alors que les caractériser permettra de construire des défenses appropriées. Bien des variations sur ce thème sont possibles, y compris avec l’aide de la synthèse artificielle de variants dont on saurait imaginer la pathogénicité pour l’homme. Depuis plus de deux décennies, des chercheurs développent des expériences de ce type, dite de « gain de fonction » (GdF). Leur interprétation repose sur l’illusion que nous savons prévoir l’évolution des êtres vivants. En réalité, ceux que nous observons aujourd’hui ont été sélectionnés au cours du temps précisément parce qu’ils conduisent toujours à des comportements imprévisibles. Une règle clé de l’évolution est que la vie, pour durer dans des circonstances qui ne peuvent être prévues, doit sans cesse faire émerger des formes innovantes. À ce caractère propre à la vie s’ajoute un imprévisible lié à l’impéritie humaine, cause de l’omniprésence des accidents de laboratoire. Or, en virologie spécialement, l’accident est la règle et non l’exception. Il faut ajouter que le caractère public de ces expériences les rend utilisables par toutes les structures malveillantes qui sont hélas répandues dans le monde. Il n’est pas difficile alors d’imaginer les conséquences catastrophiques des expériences de GdF. Nous proposons donc qu’elles soient purement et simplement interdites et que toute transgression soit sévèrement punie, en frappant d’abord au porte-monnaie, ce qui semble être la meilleure façon de faire dans nos sociétés devenues universellement vénales.

Science is founded on a method based on critical thinking. A prerequisite for this is not only a sufficient command of language but also the comprehension of the basic concepts underlying our understanding of reality. This constraint implies an awareness of the fact that the truth of the World is not directly accessible to us, but can only be glimpsed through the construction of mod- els designed to anticipate its behaviour. Because the relationship between models and reality rests on the interpretation of founding postulates and in- stantiations of their predictions (and is therefore deeply rooted in language and culture), there can be no demarcation between science and non-science. However, critical thinking is essential to ensure that the link between models and reality is gradually made more adequate to reality, based on what has already been established, thus guaranteeing that science progresses on this basis and excluding any form of relativism.

The abstract basis of modern computation is the formal description of a finite state machine, the Universal Turing Machine, based on manipulation of integers and logic symbols. In this contribution to the discourse on the computer-brain analogy, we discuss the extent to which analog computing, as performed by the mammalian brain, is like and unlike the digital computing of Universal Turing Machines. We begin with ordinary reality being a permanent dialog between continuous and discontinuous worlds. So it is with computing, which can be analog or digital, and is often mixed. The theory behind computers is essentially digital, but efficient simulations of phenomena can be performed by analog devices; indeed, any physical calculation requires implementation in the physical world and is therefore analog to some extent, despite being based on abstract logic and arithmetic. The mammalian brain, comprised of neuronal networks, functions as an analog device and has given rise to artificial neural networks that are implemented as digital algorithms but function as analog models would. Analog constructs compute with the implementation of a variety of feedback and feedforward loops. In contrast, digital algorithms allow the implementation of recursive processes that enable them to generate unparalleled emergent properties. We briefly illustrate how the cortical organization of neurons can integrate signals and make predictions analogically. While we conclude that brains are not digital computers, we speculate on the recent implementation of human writing in the brain as a possible digital path that slowly evolves the brain into a genuine (slow) Turing machine.

Pasteur’s originality in the way he developed pure research is to have understood the importance, for society, of the underlying motivation. Curiosity, of course, is a strong motivation, which explains why we seek to understand the origin of life. But, in front of the immensity of the possible choices, why not, also, choose to start from questions of economic interest (diseases of beer and wine, diseases aVecting the silk industry . . . ) Finally, of course, health is a constant preoccupation, but the diseases, which have no borders, often come from tropical countries and Asia especially. It is therefore necessary to settle there, but not to come and impose one’s point of view, but on the contrary to use the knowledge coming from the local culture in order to open new ways of understanding the reality of the world.

Synthetic biology (SynBio) covers two main areas: application engineering, exemplified by metabolic engi- neering, and the design of life from artificial building blocks. As the general public is often reluctant to embrace synthetic approaches, preferring nature to artifice, its immediate future will depend very much on the public’s reaction to the unmet needs created by the pervasive demands of sustainability. On the other hand, this reluctance should not have a negative impact on research that will now take into account the existence of the multiple transitions that cells face over time. The ages of life—birth, development, maturation, senescence and death—reflect specific key transitions and have, until now, rarely been taken into account in SynBio designs. This results in a mismatch between novelty and the very long evolutionary time that led to the existing chassis [remember that this is the common term used to describe the cellular framework as seen by synthetic biologists (de Lorenzo & Danchin, 2008)]. It also implies that, in general, transitions between growth stages will be taken into account with the appro- priate embodiment of highly specific processes. This is particularly important when adapting new models to their host, whether natural or artificial. Adaptation fol- lows two stages, short-term accommodation of new entities and long-term assimilation into the cell as a whole. This requires discrimination between classes of entities. We suggest that proteins playing the essential role of Maxwell’ demons, here named Maxwell’s dis- criminators (MxDs) to refer to their original function, will permit the assimilation and accommodation of artificial constructs. As a consequence, we can foresee that class discrimination, beyond mere recognition, will be implemented in SynBio 2.0, leading to an authentic par- adigm shift (Kuhn, 1996), based on conceptions that embody information as a genuine currency of reality.

Dans un monde dominé par les conflits, il arrive qu’il faille se défendre. L’invention des armes a évolué en parallèle avec le savoir technique, puis scientifique, et il est même arrivé que la recherche d’applications militaires ait joué un rôle moteur dans la découverte scientifique. Lorsque les armes ne servent pas à attaquer d’autres nations, leur fabrication et leur commerce se justifient morale- ment. Il faut cependant qu’elles ne puissent échapper à ceux qui les construisent et doivent en contrôler la diffusion. Facilement mise en œuvre, la guerre utilisant des organismes vivants ou ce qu’ils pro- duisent comme armes est très ancienne. Or l’originalité des êtres vivants est qu’ils se multiplient, qu’un seul individu suffit à recouvrir la Terre de ses descendants. La biologie ne se prête jamais à un usage militaire moralement défendable parce que le confinement au champ de bataille est impossible. De ce fait, les applications de la biologie ont été vite écartées du domaine de la Défense permise par les traités internationaux. La Convention de 1972 sur l’Interdiction des Armes Biologiques et à Toxines (CIABT), entrée en vigueur en 1975, est aujourd’hui signée par 183 pays (ratifiée par 175) sur un total de 193, sans compter Taïwan qui l’a ratifiée mais n’est pas reconnu par l’ONU. Elle interdit la mise au point, la fabrication, l’acquisition, le transfert, la conservation, le stockage et l’utilisation des armes bio- logiques et à toxines. Elle constitue un élément essentiel de la lutte contre la prolifération des armes de destruction massive.

Assembly of minimal genomes revealed many genes encoding unknown functions. Three overlooked functional categories account for some of them. Cells are prone to make errors and age. As a first key function, discrimination between proper and changed entities is indispensable. Discrimination requires management of information, an authentic, yet abstract, cur- rency of reality. For example proteins age, sometimes very fast. The cell must identify, then get rid of old proteins without destroying young ones. Implementing discrimination in cells leads to the second set of functions, usually ignored. Being abstract, information must nevertheless be embodied into material entities, with unavoidable idiosyncratic properties. This brings about novel unmet needs. Hence, the buildup of cells elicits specific but awkward material implementations, ‘kludges’ that become essential under particular settings, while difficult to identify. Finally, a third functional category char- acterizes the need for growth, with metabolic implementations allowing the cell to put together the growth of its cytoplasm, membranes, and genome, spanning different spatial dimensions. Solving this metabolic quandary, critical for engineering novel synthetic biology chassis, uncovered an unexpected role for CTP synthetase as the coordinator of nonhomothetic growth. Because a significant number of SynBio constructs aim at creating cell factories we expect that they will be attacked by viruses (it is not by chance that the function of the CRISPR system was identified in industrial settings). Substantiating the role of CTP, natural selection has dealt with this hurdle via synthesis of the antimetabolite 30-deoxy-30,40-didehydro- CTP, recruited for antiviral immunity in all domains of life.

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 viral clearance or disease progression, but that the immunodynamics are different in each case. As a significant proportion of the world’s population is already naturally immune or vaccinated, we also discuss the implications for secondary infections after vaccination or in the presence of immune system dysfunctions.

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 research and reflects the nature of biology itself. Annotation systems, rather than being repositories of facts, should be tools that support multiple modes of inference. By combining deduction, induction and abduction, investigators can generate hypotheses when accurate knowledge is extracted from model databases. A key stance is to depart from ‘the sequence tells the structure tells the function’ fallacy, placing function first. We illustrate our approach with examples of critical or unexpected pathways, using MicroScope to demonstrate how tools can be implemented following the principles we advocate. We end with a challenge to the reader.

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 the ribosome construction machinery, behave as would behave a material implementation of the informationmanaging agent theorized by Maxwell almost 150 years ago and commonly known as Maxwell’s demon (MxD). A core gene set encoding these functions belongs to the minimal genome required to allow the construction of an autonomous cell. These MxDs allow the cell to perform computations in an energy-efficient way that is vastly better than our contemporary computers.

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 genetic program carried by the genome. This highly abstract organisation is implemented using concrete objects and dynamics, and this is at the cost of repeated incompatibilities (frustration), which need to be sorted out by appropriate «patches». After describing the organisation of the genome into the paleome (sustaining and propagating life) and the cenome (permitting life in context), we describe some chemical hurdles that the cell as to cope with, ending with the specific case of the methionine salvage pathway

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 can lead, in the case of a given program, to a plethora of particular outcomes, because the number of possible combinations rapidly becomes enormous. Since the discoveries of Jacob and Monod, it is clear that the genes specifying the regulatory functions will be responsible for phenotypic variability, especially for the apparently ideal adaptation of a living organism to its environment, and more generally for all the genotype-bound manifestations as they unfold in time. Thus we are led to consider three particular characteristics that allow for the representation of living beings: a program, which summarizes the hereditary constraints and is, in fact, the abstract notion underlying the definition of all individuals in a given class (species); an initial state of the system that represents the context in which the program must express itself at the time of the individual's birth; and a particular outcome of each program, which coincides with individual development. The set of all outcomes constitutes the genetic envelope and allows the essential characteristics of the program to be obtained by induction. Theoretically, a structured set equivalent to the aforementioned one could be reconstructed by providing the program, the initial state, and the totality of the events of the external environment, producing any interaction whatever with the individual. As a consequence, the observation of a phenotype does not tell in any straightforward way, what is the direct consequence of the expression of a particular gene, or of a specific feature of the environment. A phenocopy is a particular example of a phenotype that is the result of a gene expression mimicking a particular gene-directed phenotype, without however corresponding to a pparticular mutation of a known gene.

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 qui peut paraître quelque peu paradoxal ou inadéquat, en décrivant, parmi la mythologie prégnance, quelque chose qui soit symétrique, et non équivalent, de la mort du père: je vais commencer par évoquer les mythes qui concernent la mort de la progéniture.

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 with this question, and the Eleatic school was dedecated to demonstrating that it would forever imprison us: appearances are discontinous, but reality is continous. Thus, the question remains central to debates in chemistry and physics, despite the remarkable attempt by the atomists to defer the problem by changing the level of description to include a macroscopic /microscopic pair destined to avert the paradox....

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 surfaces, substitution of surfaces by an RNA-world where transfer RNA played a central role, and invention of template mediated information transfer. Colonization of each niche is performed using an almost unlimited set of genes, forming the cenome. The agreement of the paleome structure with a consistent scenario for the origin of life is such that we may consider extant genomes as providing us with an archive of the origin rather than as a palimpsest where most of our past would be irremediably hidden.

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 to interact with reality via construction of self-consistent models producing predictions which can be instantiated into experiments. While the present theory of information has much to say about the program, with the creative properties of recursivity at its heart, we almost entirely lack a theory of the information supporting the machine. We suggest that the program of life codes for processes meant to trap information which comes from the context provided by the environment of the machine.

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 result in futile influx/efflux cycles. Versatile modification enzymes with low sensitivity solve the problem if the modified metabolite is the one exported by MDR permeases. This may account for the pervasive presence of acetyl-transferases, such as LacA, associated to acetyl-metabolite exporters. This scenario of constraints imposed by efficient influx of metabolites provides us with a model that should be followed when constructing synthetic cells.

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 is driven, in many proteomes, by the AANbox of the genetic code, suggesting some functional biochemical relationship between asparagine and lysine. Less-significant biases are driven by the rare amino acids, cysteine and tryptophan. Some allow identification of species-specific functions or localisation such as surface or exported proteins. Errors in genome annotations are also revealed by correspondence analysis, making it useful for quality control and correction.

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 neuromuscular junction is proposed and the basic selective aspect of learning emphasized.

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 developed what we might call ‘motivated’ research. How is research motivated and by what? By definition, scientists are citizens and members of the general public and, like the public, they are motivated by two forces: on the one hand, in Rudyard Kipling's words, “man's insatiable curiosity”; on the other hand, a desire for maintaining and improving their well‐being. These are not contradictory to one another; curiosity nourishes dreams of a brighter future and leads to discoveries that contribute to well‐being.

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 messages is a tiny part of what information is. Because we use language, built on the exchange of sequences of symbols, exactly as programs are exchanged in computers, linguists often saw the brain as a Turing Machine. But language is deeply associated to meaning, so that beside grammatical syntactic structures, there may exist a variety of superimposed contexts which transmit information mediated by channels that are not those usually considered.

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, precluding strict accuracy. Hence, for each regular pathway, a wealth of variants inputs and produces metabolites that are similar to but not the exact replicas of core metabolites. As corollary, a shadow, paralogous metabolism, is associated to standard metabolism. We focus on a logic of paralogous metabolism based on diversion of the core metabolic mimics into pathways where they are modified to minimize their input in the core pathways where they create havoc. We propose that a significant proportion of paralogues of well-characterized enzymes have evolved as the natural way to cope with paralogous metabolites. A second type of denouement uses a process where protecting/deprotecting unwanted metabolites - conceptually similar to the procedure used in the laboratory of an organic chemist - is used to enter a completely new catabolic pathway.

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 and molecular and cell biology—we feel that information as an essential aspect of life has been neglected, or at least misunderstood. We therefore summon Maxwell’s Demon and its distant relative the ratchet, and apply these to biology.

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 life yield examples of entities that may be antifragile. One such example is proteins with flexible regions that can undergo functional alteration of their side residues or backbone and thus implement the tinkering that leads to antifragility. This in-built property of the cell chassis must be taken into account when considering construction of cell factories driven by engineering principles.

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 deaminase, where the first hypothesis of the binding of a regulator molecule on the enzyme could be located at a place different from the catalytic substrate binding site was presented (hence the word allostery coined by Monod in the introduction of the conference where the work of Changeux was presented). Symmetry is not a critical component of the concept of allostery.

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 cytoplasm, and an outside. The cell envelope is more or less complicated in bacteria, and it is much more complicated in organisms made of cells with a nucleus (eukaryotes). Second, the machine also requires dynamic chemical processes, collectively named metabolism, that can be split into intermediary metabolism, managing chemical transformations and transport of small building blocks and management of energy (often with a rotating nanomachine, ATP synthase), and the macromolecule synthesis, salvage and turnover machinery which uses a variety of nanomachines, the ribosome being the most prominent one. The second entity which needs to be associated to life is the genetic program, in the form of the genome, composed of one or several chromosomes made of DNA. This is the entity which associates most clearly to information. Natural selection uses information in a particular way: it is a process that uses energy to prevent degradation of any functional entity. This process keeps building up novel information within organisms.

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 brought to biological design. These should endow functional building blocks with a pre-specified level of confidence for bespoke biosystems engineering. However, in the absence of more fundamental knowledge, fine-tuning necessarily relies on evolutionary/combinatorial gravitation toward a fixed objective.