Very large databases are a major opportunity for science and data analytics is a remarkable new field of investigation in computer science. The effectiveness of these tools is used to support a “philosophy” against the scientific method as developed throughout history. According to this view, computer-discovered correlations should replace understanding and guide prediction and action. Consequently, there will be no need to give scientific meaning to phenomena, by proposing, say, causal relations, since regularities in very large databases are enough: “with (...) enough data, the numbers speak for themselves”. The “end of science” is proclaimed. Using classical results from ergodic theory, Ramsey theory and algorithmic information theory, we show that this “philosophy” is wrong. For example, we prove that very large databases have to contain arbitrary correlations. These correlations appear only due to the size, not the nature, of data. They can be found in “randomly” generated, large enough databases, which—as we will prove—implies that most correlations are spurious. Too much information tends to behave like very little information. The scientific method can be enriched by computer mining in immense databases, but not replaced by it. (shrink)

This authored monograph introduces a genuinely theoretical approach to biology. Starting point is the investigation of empirical biological scaling including their variability, which is found in the literature, e.g. allometric relationships, fractals, etc. The book then analyzes two different aspects of biological time: first, a supplementary temporal dimension to accommodate proper biological rhythms; secondly, the concepts of protension and retention as a means of local organization of time in living organisms. Moreover, the book investigates the role of symmetry in biology, (...) in view of its ubiquitous importance in physics. In relation with the notion of extended critical transitions, the book proposes that organisms and their evolution can be characterized by continued symmetry changes, which accounts for the irreducibility of their historicity and variability. The authors also introduce the concept of anti-entropy as a measure for the potential of variability, being equally understood as alterations in symmetry. By this, the book provides a mathematical account of Gould's analysis of phenotypic complexity with respect to biological evolution. The target audience primarily comprises researchers interested in new theoretical approaches to biology, from physical, biological or philosophical backgrounds, but the book may also be beneficial for graduate students who want to enter this field. (shrink)

The dependence on history of both present and future dynamics of life is a common intuition in biology and in humanities. Historicity will be understood in terms of changes of the space of possibilities as well as by the role of diversity in life’s structural stability and of rare events in history formation. We hint to a rigorous analysis of “path dependence” in terms of invariants and invariance preserving transformations, as it may be found also in physics, while departing from (...) the physico-mathematical analyses. The idea is that the invariant traces of the past under organismal or ecosystemic transformations contribute to the understanding of present and future states of affairs. This yields a peculiar form of unpredictability in biology, at the core of novelty formation: the changes of observables and pertinent parameters may depend also on past events. In particular, in relation to the properties of synchronic measurement in physics, the relevance of diachronic measurement in biology is highlighted. This analysis may a fortiori apply to cognitive and historical human dynamics, while allowing to investigate some general properties of historicity in biology. (shrink)

The human attempts to access, measure and organize physical phenomena have led to a manifold construction of mathematical and physical spaces. We will survey the evolution of geometries from Euclid to the Algebraic Geometry of the 20th century. The role of Persian/Arabic Algebra in this transition and its Western symbolic development is emphasized. In this relation, we will also discuss changes in the ontological attitudes toward mathematics and its applications. Historically, the encounter of geometric and algebraic perspectives enriched the mathematical (...) practices and their foundations. Yet, the collapse of Euclidean certitudes, of over 2300 years, and the crisis in the mathematical analysis of the 19th century, led to the exclusion of “geometric judgments” from the foundations of Mathematics. After the success and the limits of the logico-formal analysis, it is necessary to broaden our foundational tools and re-examine the interactions with natural sciences. In particular, the way the geometric and algebraic approaches organize knowledge is analyzed as a cross-disciplinary and cross-cultural issue and will be examined in Mathematical Physics and Biology. We finally discuss how the current notions of mathematical (phase) “space” should be revisited for the purposes of life sciences. (shrink)

Symmetries play a major role in physics, in particular since the work by E. Noether and H. Weyl in the first half of last century. Herein, we briefly review their role by recalling how symmetry changes allow to conceptually move from classical to relativistic and quantum physics. We then introduce our ongoing theoretical analysis in biology and show that symmetries play a radically different role in this discipline, when compared to those in current physics. By this comparison, we stress that (...) symmetries must be understood in relation to conservation and stability properties, as represented in the theories. We posit that the dynamics of biological organisms, in their various levels of organization, are not just processes, but permanent (extended, in our terminology) critical transitions and, thus, symmetry changes. Within the limits of a relative structural stability (or interval of viability), variability is at the core of these transitions. (shrink)

This personal, yet scientific, letter to Alan Turing, reflects on Turing's personality in order to better understand his scientific quest. It then focuses on the impact of his work today. By joining human attitude and particular scientific method, Turing is able to “immerse himself” into the phenomena on which he works. This peculiar blend justifies the epistolary style. Turing makes himself a “human computer”, he lives the dramatic quest for an undetectable imitation of a man, a woman, a machine. He (...) makes us see the continuous deformations of a material action/reaction/diffusion dynamics of hardware with no software. Each of these investigations opens the way to new scientific paths with major consequences for contemporary live and for knowledge. The uses and the effects of these investigations will be discussed: the passage from classical AI to today's neural nets, the relevance of non-linearity in biological dynamics, but also their abuses, such as the myth of a computational world, from a Turing-machine like universe to an encoded homunculus in the DNA. It is shown that these latter ideas, which are sometimes even made in Turing's name, contradict his views. (shrink)

This article proposes an abstract mathematical frame for describing some features of cognitive and biological time. We focus here on the so called “extended present” as a result of protentional and retentional activities (memory and anticipation). Memory, as retention, is treated in some physical theories (relaxation phenomena, which will inspire our approach), while protention (or anticipation) seems outside the scope of physics. We then suggest a simple functional representation of biological protention. This allows us to introduce the abstract notion of (...) “biological inertia”. (shrink)

The physical singularity of life phenomena is analyzed by means of comparison with the driving concepts of theories of the inert. We outline conceptual analogies, transferals of methodologies and theoretical instruments between physics and biology, in addition to indicating significant differences and sometimes logical dualities. In order to make biological phenomenalities intelligible, we introduce theoretical extensions to certain physical theories. In this synthetic paper, we summarize and propose a unified conceptual framework for the main conclusions drawn from work spanning a (...) book and several articles, quoted throughout. (shrink)

The “DNA is a program” metaphor is still widely used in Molecular Biology and its popularization. There are good historical reasons for the use of such a metaphor or theoretical model. Yet we argue that both the metaphor and the model are essentially inadequate also from the point of view of Physics and Computer Science. Relevant work has already been done, in Biology, criticizing the programming paradigm. We will refer to empirical evidence and theoretical writings in Biology, although our arguments (...) will be mostly based on a comparison with the use of differential methods (in Molecular Biology: a mutation or alike is observed or induced and its phenotypic consequences are observed) as applied in Computer Science and in Physics, where this fundamental tool for empirical investigation originated and acquired a well-justified status. In particular, as we will argue, the programming paradigm is not theoretically sound as a causal(as in Physics) or deductive(as in Programming) framework for relating the genome to the phenotype, in contrast to the physicalist and computational grounds that this paradigm claims to propose. (shrink)

We propose a reflection on the construction of scientific knowledge and in so doing an image of this knowledge. This will allow us to develop a comparative analysis of some of the main principles underpinning the constitution of the different sciences. We will highlight the role of critical thought in science, or even “negative results,” which pose limits and hence open new trajectories. In particular, we will address a misleading point of view, based on some informal concepts taken from computer (...) science, which dominates the biological imaginary. An “ethics of knowledge” will follow, as a critical and open perspective, capable of taking on the well-intentioned responsibility of proposing universal, though not absolute, principles of knowledge. (shrink)

This paper proposes an abstract mathematical frame for describing some features of biological time. The key point is that usual physical (linear) representation of time is insufficient, in our view, for the understanding key phenomena of life, such as rhythms, both physical (circadian, seasonal …) and properly biological (heart beating, respiration, metabolic …). In particular, the role of biological rhythms do not seem to have any counterpart in mathematical formalization of physical clocks, which are based on frequencies along the usual (...) (possibly thermodynamical, thus oriented) time. We then suggest a functional representation of biological time by a 2-dimensional manifold as a mathematical frame for accommodating autonomous biological rhythms. The “visual” representation of rhythms so obtained, in particular heart beatings, will provide, by a few examples, hints towards possible applications of our approach to the understanding of interspecific differences or intraspecific pathologies. The 3- dimensional embedding space, needed for purely mathematical reasons, allows to introduce a suitable extra-dimension for “representation time”, with a cognitive significance. (shrink)

This short paper is meant to be an introduction to the ‘Letter to Alan Turing’ that follows it. It summarizes some basic ideas in information theory and very informally hints at their mathematical properties. In order to introduce Turing’s two main theoretical contributions, in Theory of Computation and in Morphogenesis, the fundamental divide between discrete vs. continuous structures in mathematics is presented, as it is also a divide in his scientific life. The reader who is familiar with these notions, and (...) is convinced that they are relevant in the mathematical understanding of phenomena, may skip this introduction and go directly to the Letter. (shrink)

n this text, we revisit part of the analysis of anti-entropy in Bailly and Longo (2009} and develop further theoretical reflections. In particular, we analyze how randomness, an essential component of biological variability, is associated to the growth of biological organization, both in ontogenesis and in evolution. This approach, in particular, focuses on the role of global entropy production and provides a tool for a mathematical understanding of some fundamental observations by Gould on the increasing phenotypic complexity along evolution. Lastly, (...) we analyze the situation in terms of theoretical symmetries, in order to further specify the biological meaning of anti-entropy as well as its strong link with randomness. (shrink)

Action dans l'espace, l'infini, la cognition humaine (link to the English text).

We informally discuss some recent results on the incompleteness of formal systems. These theorems, which are of great importance to contemporary mathematical epistemology, are proved using a variety of conceptual tools provably stronger than those of finitary axiomatisations. Those tools require no mathematical ontology, but rather constitute particularly concrete human constructions and acts of comprehending infinity and space rooted in different forms of knowledge. We shall also discuss, albeit very briefly, the mathematical intelligence both of God and of computers. We (...) hope in this manner to help the reader overcome formalist reductionism, while avoiding naive Platonist ontologies, typical symptoms of Godelitis which affected many in the last seventy years. (shrink)

BIG DATA AND ARTIFICIAL INTELLIGENCE: A LOOK INTO THE FUTURE To say or write something innovative on the ongoing revolution in the fields of Big Data and Artificial Intelligence is very difficult. The advent of these two new technologies is in fact among the most relevant events in human history since in a little more than a decade it will likely lead to the creation of the First Artificial Intelligence of the Fourth level: i.e capable to think and create autonomously. (...) This is a strong statement but like it or not is also irrefutable and fully compatible with the current technological trends and with what is happening right now, in front of our eyes. For the time being, however, we are dealing just with a weak Artificial Intelligence deeply rooted in Big Data and Big Data Analytics. Even so, however, the epochal changes which are currently taking place in the social, economic, and political structure of our world, have no historical equivalent. In this essay, after a short introduction (for the nonprofessional) of Machine Learning and of the basics of the weak Artificial Intelligence, I will try to explain why Artificial Intelligence and Big Data inextricably connect to each other. I will also try to summarise some among the many positive and negative aspects of the problem. (shrink)

The foundation of Mathematics is both a logico-formal issue and an epistemological one. By the first, we mean the explicitation and analysis of formal proof principles, which, largely a posteriori, ground proof on general deduction rules and schemata. By the second, we mean the investigation of the constitutive genesis of concepts and structures, the aim of this paper. This “genealogy of concepts”, so dear to Riemann, Poincaré and Enriques among others, is necessary both in order to enrich the foundational analysis (...) with an often disregarded aspect (the cognitive and historical constitution of mathematical structures) and because of the provable incompleteness of proof principles also in the analysis of deduction. For the purposes of our investigation, we will hint here to a philosophical frame as well as to some recent experimental studies on numerical cognition that support our claim on the cognitive origin and the constitutive role of mathematical intuition. (shrink)

La cognition humaine paraît étroitement liée à la structure de l'espace et du temps relativement auxquels le corps, le geste, l'intelligibilité semblent devoir se déterminer. Pourtant, ce qui, après les approches physico-mathématiques de Galilée et de Newton, fut caractérisé par Kant comme formes de l'intuition sensible, n'a cessé au cours des siècles qui suivirent de se trouver remis en cause dans leur saisie première par les développements théoriques. En mathématiques d'abord, avec les géométries non-euclidiennes, en physique ensuite, où relativité générale (...) puis théories quantiques et critiques ont dû remanier profondément l'objectivité de ces concepts pour en faire des catégories, certes toujours aussi essentielles, mais de plus en plus contre-intuitives, et maintenant en biologie où la temporalité, notamment, et la causalité se révèlent largement différentes de celles de la physique. C'est ce que nous tentons de présenter et de discuter dans ce texte en vue d'en dégager la pertinence pour la cognition elle-même. (shrink)

The intellectual act of imposing borders to contain and delimit objects has been a constituent factor in physics since its origins, and is also fundamental for philosophical reflection. However, the characteristics of the conceptual universe thus constructed (tendency towards the ideal limit, invariance in variation, a conception of matter as residue, etc.) seem inadequate in biology. The essential characteristic of the living thing is, in fact, that of having a history: that is, of being the concrete trace of a memory. (...) Making an epistemology of the living thing (and not of the inert) means identifying new categories which, being radically antithetical to disembodied notions like that of program and information, take account of the unpredictability and creativity which time introduces. This essay aims to bring some of these fundamental categories into focus. (shrink)

Nel presente testo cercherò principalmente di esplicitare la correlazione tra le mie ricerche, così come ho cercato di riassumerle nel testo su La ragionevole efficacia della matematica, e l’impostazione vareliana nei confronti delle scienze cognitive. Nel tentativo di far questo, intendo prendere spunto da un aneddoto che, a dire il vero, pare sia effettivamente accaduto. Si racconta che, intorno ai sette o otto anni, il piccolo Gauss si trovò di fronte un maestro severissimo che, come puniz...

Dans la mythologie grecque, Prométhée - le 'prévoyant' - déroba le feu aux dieux et le transmit aux hommes. Zeus, courroucé par ce transfert technologique, condamna Prométhée à un châtiment itéré à l'identique, à l'infini, algorithmique. Le problème que pose l'ancien mythe est celui des limites de la connaissance. En termes modernes, jusqu'à quel point pouvons-nous transformer la nature sans une connaissance des conséquences de nos actions sur elle? Cette question nous pousse à analyser les limites des sciences : à (...) une techno-science devenue toujours plus invasive, la science répond en se donnant à elle-même des limites"--Page 4 of cover. (shrink)

The first part of this paper highlights some key aspects of the differences in the use of mathematical tools in physics and in biology. Scientific knowledge is viewed as a network of interactions, some than as a hierarchically organized structure where mathematics would display the essence of phenomena. The concept of "unity" in the biological phenomenon is then discussed. In the second part, a foundational issue in mathematics is revisited, following recent perspective in the physiology of action. The relevance of (...) the historical formation of mathematical concepts is stressed in several parts. (shrink)