What role does non-genetic inheritance play in evolution? In recent work we have independently and collectively argued that the existence and scope of non-genetic inheritance systems, including epigenetic inheritance, niche construction/ecological inheritance, and cultural inheritance—alongside certain other theory revisions—necessitates an extension to the neo-Darwinian Modern Synthesis (MS) in the form of an Extended Evolutionary Synthesis (EES). However, this argument has been challenged on the grounds that non-genetic inheritance systems are exclusively proximate mechanisms that serve the ultimate function of calibrating organisms (...) to stochastic environments. In this paper we defend our claims, pointing out that critics of the EES (1) conflate non-genetic inheritance with early 20th-century notions of soft inheritance; (2) misunderstand the nature of the EES in relation to the MS; (3) confuse individual phenotypic plasticity with trans-generational non-genetic inheritance; (4) fail to address the extensive theoretical and empirical literature which shows that non-genetic inheritance can generate novel targets for selection, create new genetic equilibria that would not exist in the absence of non-genetic inheritance, and generate phenotypic variation that is independent of genetic variation; (5) artificially limit ultimate explanations for traits to gene-based selection, which is unsatisfactory for phenotypic traits that originate and spread via non-genetic inheritance systems; and (6) fail to provide an explanation for biological organization. We conclude by noting ways in which we feel that an overly gene-centric theory of evolution is hindering progress in biology and other sciences. (shrink)

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. (shrink)

The linguistic foundations of science and technology include many terms that have been borrowed from ancient languages. In the case of terms with origins in the Greek language, the modern meaning can often differ significantly from the original one. Here we use the PubMed database to demonstrate the prevalence of words of Greek origin in the language of modern science, and call for scientists to exercise care when coining new terms.

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. (shrink)

Background: Microbiome biomarker discovery for patient diagnosis, prognosis, and risk evaluation is attracting broad interest. Selected groups of microbial features provide signatures that characterize host disease states such as cancer or cardio-metabolic diseases. Yet, the current predictive models stemming from machine learning still behave as black boxes and seldom generalize well. Their interpretation is challenging for physicians and biologists, which makes them difficult to trust and use routinely in the physician-patient decision-making process. Novel methods that provide interpretability and biological insight (...) are needed. Here, we introduce "predomics", an original machine learning approach inspired by microbial ecosystem interactions that is tailored for metagenomics data. It discovers accurate predictive signatures and provides unprecedented interpretability. The decision provided by the predictive model is based on a simple, yet powerful score computed by adding, subtracting, or dividing cumulative abundance of microbiome measurements. -/- Results: Tested on >100 datasets, we demonstrate that predomics models are simple and highly interpretable. Even with such simplicity, they are at least as accurate as state-of-the-art methods. The family of best models, discovered during the learning process, offers the ability to distil biological information and to decipher the predictability signatures of the studied condition. In a proof-of-concept experiment, we successfully predicted body corpulence and metabolic improvement after bariatric surgery using pre-surgery microbiome data. -/- Conclusions: Predomics is a new algorithm that helps in providing reliable and trustworthy diagnostic decisions in the microbiome field. Predomics is in accord with societal and legal requirements that plead for an explainable artificial intelligence approach in the medical field. (shrink)

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. (shrink)

Vous menez depuis plusieurs années des enquêtes sur le personnel politique en France, avec l’ambition de reconsidérer la notion de « professionnel » de la politique et par extension les ressorts d’une « professionnalisation » de la vie politique en France. Un point de départ, semble-t-il, de votre réflexion porte sur le fait que ces termes servent souvent (à l’instar du vocable péjoratif de « politicien » auquel ils se substituent souvent) à dévaloriser le personnel politique. Ils avaient pourtant été (...) conçus par les sciences sociales pour mettre à distance tout jugement de valeur à propos des élus. On pense bien sûr à Max Weber, mais aussi aux travaux fondateurs de Daniel Gaxie ou Jacques Lagroye, notamment. Comment vos propres travaux se situent-ils par rapport à la dimension normative inévitablement attachée à cet objet qu’est le « métier » de député? Il est vrai que je mène une critique des « professionnels de la politique », mais pas tout à fait dans le sens de celle qui domine... (shrink)

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. (shrink)

Western European liberal democracies have recently enacted laws that prohibit the diffusion of fake news on social media. Yet, many consider that such laws are incompatible with freedom of expression. In this paper, I argue that democratic governments have strong pro tanto reasons to prohibit fake news, and that doing so is compatible with free speech. First, I show that fake news disrupts a mutually beneficial form of epistemic dependence in which members of the public are engaged with journalists. Second, (...) I contend that laws against fake news enhance rather than thwart personal autonomy. If these suggestions are plausible, then the same considerations about truth and autonomy that underpin the value of free speech give us reasons to prohibit fake news. (shrink)

étienne Balibar has been one of Europe's most important philosophical and political thinkers since the 1960s. His work has been vastly influential on both sides of the Atlantic throughout the humanities and the social sciences. In We, the People of Europe?, he expands on themes raised in his previous works to offer a trenchant and eloquently written analysis of "transnational citizenship" from the perspective of contemporary Europe. Balibar moves deftly from state theory, national sovereignty, and debates on multiculturalism and (...) European racism, toward imagining a more democratic and less state-centered European citizenship. Although European unification has progressively divorced the concepts of citizenship and nationhood, this process has met with formidable obstacles. While Balibar seeks a deep understanding of this critical conjuncture, he goes beyond theoretical issues. For example, he examines the emergence, alongside the formal aspects of European citizenship, of a "European apartheid," or the reduplication of external borders in the form of "internal borders" nurtured by dubious notions of national and racial identity. He argues for the democratization of how immigrants and minorities in general are treated by the modern democratic state, and the need to reinvent what it means to be a citizen in an increasingly multicultural, diversified world. A major new work by a renowned theorist, We, the People of Europe? offers a far-reaching alternative to the usual framing of multicultural debates in the United States while also engaging with these debates. (shrink)

Major difficulties for readers of Foucault’s The Order of Things concern the historical function and the logical construction of the episteme. Our proposal is to link it with another notion, the ‘point of heresy’, less frequently addressed. This leads to asserting that irreconcilable dilemmas are in fact determined by the type of rationality governing the emergence of common objects of knowledge. It also introduces a possibility of ‘walking on two roads’: a dialogical adventure within rationality. Foucault is not content with (...) either accepting or rejecting the ‘transcendental’ question ‘What is Man?’: with the help of quasi-transcendental categories performing a ‘transdisciplinary’ function, he wants to reach the ‘heretical’ point where anthropology becomes historicity within the horizon of finitude. (shrink)

If citizens are to make enlightened collective decisions, they need to rely on true factual beliefs, but misinformation impairs their ability to do so. Although some cases of misinformation are deliberate and amount to propaganda, cases of inadvertent misinformation are just as problematic in affecting the beliefs and behavior of democratic citizens. A review of empirical evidence suggests that this is a serious problem that cannot entirely be corrected by means of deliberation.

In a recent contribution to conceptual ethics, Joshua Habgood-Coote argues that philosophers should refrain from using the term “fake news,” which is commonly employed in public discussions focusing on the epistemic health of democracies. In this short discussion note, I take issue with this claim, discussing each of the three arguments advanced by Coote to support the conclusion that we should abandon this concept. First, I contend that although “fake news” is a contested concept, there is significant agreement among contemporary (...) philosophers about its key feature. Second, I argue against the claim that “fake news” is an unnecessary concept by underlying that it is not reducible to other terms we customarily use to describe the epistemic dysfunctions of democracies. Lastly, I suggest that using the term “fake news” need not serve propagandistic aims, and that philosophers can use this concept without engaging in epistemic policing, that is, commanding their interlocutors not to believe specific news stories or sources. (shrink)

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. (shrink)

Quel rapport entre l'existence d'une oeuvre d'art et celle d'un être vivant? Entre l'existence de l'atome et celle d'une valeur comme la solidarité? Ces questions sont les nôtres à chaque fois qu'une réalité est instaurée, prend consistance et vient à compter dans nos vies, qu'il s'agisse d'un morceau de musique, d'un amour ou de Dieu en personne. Comme James ou Deleuze, Souriau défend méthodiquement la thèse d'un pluralisme existentiel. Il y a, en effet, différentes manières d'exister, et même différents degrés (...) ou intensités d'existence : des purs phénomènes aux choses objectivées, en passant par le virtuel et le " sur-existant " dont témoignent les œuvres de l'esprit ou de l'art, tout comme le fait même de la morale. L'existence est polyphonique, et le monde s'en trouve considérablement enrichi et élargi. Outre ce qui existe au sens ordinaire du terme, il faut compter avec toutes sortes d'états virtuels ou fugaces, de domaines transitionnels, de réalités ébauchées, en devenir, qui sont autant d'" intermondes ". Servi par une érudition stupéfiante qui lui permet de traverser d'un pas allègre toute l'histoire de la philosophie, Souriau donne les éléments d'une grammaire de l'existence. Mais son enquête se veut aussi une introduction à " la pratique de l'art d'exister ". A quoi nous attachons-nous précisément lorsque nous aimons un être? A quoi nous engageons-nous lorsque nous nous identifions à un personnage de roman, lorsque nous valorisons une institution ou adhérons à une théorie? Et finalement, quel(s) mode(s) d'existence(s) sommes-nous capables d'envisager et d'expérimenter pour nous-mêmes? Questions métaphysiques, questions vitales. Cette nouvelle édition est précédée d'une présentation d'Isabelle Stengers et Bruno Latour intitulée " Le sphinx de l'œuvre ". Elle inclut également un article d'Étienne Souriau, " Du mode d'existence de l'œuvre à faire " (1956). (shrink)

"As one of Louis Althusser's most brilliant students in the 1960s, Etienne Balibar contributed to the theoretical collective masterpiece of Reading Capital. Since then he has established himself amongst the most subtle philosophical and political thinkers in France. In Politics and the Other Scene Balibar deepens and extends the work he first developed with Immanuel Wallerstein in Race, Nation, Class. Exploring the theme of universalism and difference, he addresses questions such as "European racism, " the notion of the border, whether (...) a European citizenship is possible or desirable, violence and politics, identity and emancipation"--provided by publisher. (shrink)

Quel rapport entre l'existence d'une oeuvre d'art et celle d'un être vivant? Entre l'existence de l'atome et celle d'une valeur comme la solidarité? Ces questions sont les nôtres à chaque fois qu'une réalité est instaurée, prend consistance et vient à compter dans nos vies, qu'il s'agisse d'un morceau de musique, d'un amour ou de Dieu en personne. Comme James ou Deleuze, Souriau défend méthodiquement la thèse d'un pluralisme existentiel. Il y a, en effet, différentes manières d'exister, et même différents degrés (...) ou intensités d'existence : des purs phénomènes aux choses objectivées, en passant par le virtuel et le " sur-existant " dont témoignent les œuvres de l'esprit ou de l'art, tout comme le fait même de la morale. L'existence est polyphonique, et le monde s'en trouve considérablement enrichi et élargi. Outre ce qui existe au sens ordinaire du terme, il faut compter avec toutes sortes d'états virtuels ou fugaces, de domaines transitionnels, de réalités ébauchées, en devenir, qui sont autant d'" intermondes ". Servi par une érudition stupéfiante qui lui permet de traverser d'un pas allègre toute l'histoire de la philosophie, Souriau donne les éléments d'une grammaire de l'existence. Mais son enquête se veut aussi une introduction à " la pratique de l'art d'exister ". A quoi nous attachons-nous précisément lorsque nous aimons un être? A quoi nous engageons-nous lorsque nous nous identifions à un personnage de roman, lorsque nous valorisons une institution ou adhérons à une théorie? Et finalement, quel(s) mode(s) d'existence(s) sommes-nous capables d'envisager et d'expérimenter pour nous-mêmes? Questions métaphysiques, questions vitales. Cette nouvelle édition est précédée d'une présentation d'Isabelle Stengers et Bruno Latour intitulée " Le sphinx de l'œuvre ". Elle inclut également un article d'Étienne Souriau, " Du mode d'existence de l'œuvre à faire " (1956). (shrink)

Kant’s discussion of the highest good is subject to continuous disagreement between the proponents of two interpretations of this concept. According to the secular interpretation, Kant conceived of the highest good as a political ideal which can be realized through human agency alone, albeit only from the Critique of the Power of Judgement onwards. By way of contrast, proponents of the theological interpretation find Kant’s treatment of the highest good in his later works to be wholly coherent with the discussions (...) of this concept found in the second Critique. In their view, however, Kant never conceived of the highest good as a political ideal, and some go as far as to argue that it is the work of God alone. In this article, I defend a theologico-political account of the highest good that avoids the pitfalls of both readings. (shrink)

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. (shrink)

Answering a question of B. Karsenti on the relation between ontology and politics, E. Balibar reaffirms the irreducible character of politics, including the most philosophical objects. Between the two ontological and transcendental poles of politics, it appears in order to articulate the political and the anthropological. The social relations, functioning by introducing differences in the species, are constitutive of the question of violence that is at the heart of the it-reducibility of politics.

First published in French in 2010, _Equaliberty_ brings together essays by Étienne Balibar, one of the preeminent political theorists of our time. The book is organized around _equaliberty_, a term coined by Balibar to connote the tension between the two ideals of modern democracy: equality and liberty. He finds the tension between these different kinds of rights to be ingrained in the constitution of the modern nation-state and the contemporary welfare state. At the same time, he seeks to keep (...) rights discourse open, eschewing natural entitlements in favor of a deterritorialized citizenship that could be expanded and invented anew in the age of globalization. Deeply engaged with other thinkers, including Arendt, Rancière, and Laclau, he posits a theory of the polity based on social relations. In _Equaliberty_ Balibar brings both the continental and analytic philosophical traditions to bear on the conflicted relations between humanity and citizenship. (shrink)

Il saggio affronta la relazione tra nazionalismo e razzismo ruotando attorno alle nozioni di etnicità fittizia e di schema genealogico, rinvianti all’idea che la nazione debba trovare un meccanismo, istituzionale e immaginario, per trasferire e riprodurre al livello politico la funzione simbolica che lega il susseguirsi delle generazioni sotto il segno del ‘retaggio culturale’ e della ‘identità ereditaria’. Da un’analisi attenta risulta come tali nozioni siano il residuo dell’idea di ‘razza’ dopo che la sua applicazione alla violenta discriminazione dei soggetti (...) coloniali, o dei discendenti degli schiavi, o dell’alterità etnica, è stata delegittimata. Si può comprendere come la nozione di razza, qualunque sia la giustificazione biologica adottata, non sia mai stata altro che una costruzione mitologica volta ad autorizzare il pensiero che riproduzione, trasmissione, educazione, memoria, tradizione, avvengano nei limiti di una comunità dotata di una identità riconoscibile.This essay deals with the relationship between nationalism and racism, and it revolves around the notions of fictitious ethnicity and genealogical scheme. Both these notions refer to the idea that the nation must find an institutional and imaginary mechanism in order to transfer and reproduce at a political level the symbolic function which binds the succession of generations under the sign of ‘cultural heritage’ and ‘hereditary identity’. A careful analysis shows how these notions are the residue of the idea of ‘race’ after the de-legitimation of its application to the violent discrimination of colonial subjects, or descendants of slaves, or ethnic alterity. It can be understood how the notion of race, whatever biological justification is adopted, was nothing else than a mythological construction, its aim being to support the idea that reproduction, transmission, education, memory, tradition, occur within the limits of a community with a recognizable identity. (shrink)