On biological individuation.

In this paper, we understand the emergence of life as a pure individuation process. Individuation already occurs in open thermodynamics systems near equilibrium. We understand such open systems, as already recursively characterized (R1) by the relation between their internal properties, and their boundary conditions. Second, global properties emerge in such physical systems. We interpret this change as the fact that their structure is the recursive result of their operations (R2). We propose a simulation of the emergence of life in Earth by a mapping (R) through which (R1R2) operators are applied to themselves, so that RN = (R1R2)N. We suggest that under specific thermodynamic (open systems out of equilibrium) and chemical conditions (autocatalysis, kinetic dynamic stability), this mapping can go up to a limit characterized by a fixed-point equation: [Formula: see text]. In this equation, ([Formula: see text]) symbolizes a regime of permanent resonance characterizing the biosphere, as open from inside, by the recursive differential relation between the biosphere and all its holobionts. As such the biosphere is closed on itself as a pure differential entity. ([Formula: see text]) symbolizes the regime of permanent change characterizing the emergence of evolution in the biosphere. As such the biosphere is closed on itself, by the principle of descent with modifications, and by the fact that every holobiont evolves in a niche, while evolving with it.

Symmetry breaking and functional incompleteness in biological systems.

Symmetry-based explanations using symmetry breaking (SB) as the key explanatory tool have complemented and replaced traditional causal explanations in various domains of physics. The process of spontaneous SB is now a mainstay of contemporary explanatory accounts of large chunks of condensed-matter physics, quantum field theory, nonlinear dynamics, cosmology, and other disciplines. A wide range of empirical research into various phenomena related to symmetries and SB across biological scales has accumulated as well. Led by these results, we identify and explain some common features of the emergence, propagation, and cascading of SB-induced layers across the biosphere. These features are predicated on the thermodynamic openness and intrinsic functional incompleteness of the systems at stake and have not been systematically analyzed from a general philosophical and methodological perspective. We also consider possible continuity of SB across the physical and biological world and discuss the connection between Darwinism and SB-based analysis of the biosphere and its history.

From Biological Determination to Entangled Causation.

Biologists and philosophers often use the language of determination in order to describe the nature of developmental phenomena. Accounts in terms of determination have often been reductionist. One common idea is that DNA is supposed to play a special explanatory role in developmental explanations, namely, that DNA is a developmental determinant. In this article we try to make sense of determination claims in developmental biology. Adopting a manipulationist approach, we shall first argue that the notion of developmental determinant is causal. We suggest that two different theses concerning developmental determination can be articulated: determination of occurrence and structural determination. We shall argue that, while the first thesis is problematic, the second, opportunely qualified, is feasible. Finally, we shall argue that an analysis of biological causation in terms of determination cannot account for entangled dynamics. Characterising causal entanglement as a particular kind of interactive causation whereby difference-making causes ascribable to different levels of biological organisation influence a particular ontogenetic outcome, we shall, via two illustrative examples, diagnose some potential limits of a reductionist, molecular and intra-level understanding of biological causation.

Toward a theory of organisms: Three founding principles in search of a useful integration.

Organisms, be they uni- or multi-cellular, are agents capable of creating their own norms; they are continuously harmonizing their ability to create novelty and stability, that is, they combine plasticity with robustness. Here we articulate the three principles for a theory of organisms, namely: the default state of proliferation with variation and motility, the principle of variation and the principle of organization. These principles profoundly change both biological observables and their determination with respect to the theoretical framework of physical theories. This radical change opens up the possibility of anchoring mathematical modeling in biologically proper principles.

From physical to biological individuation.

In this paper, we insist on stressing the epistemic and metaphysical difference between individual and individuation, a distinction originally developed by Gilbert Simondon. Individuation occurs in complex physical systems by the coupling (R1) between the system and its outside conditions. As such the system is not well defined by its sole constituents. Let's characterize (R2) as follows: the system is not entirely defined by its structure at a given time because this structure will change and global emergent properties will appear, as in the paradigmatic example of phase transition. Thus physical individuation is defined both by the coupling of a physical system with its environment (R1) and by its diachronic dynamics taking place (R2). We interpret biological individuation as a second order one, i.e. as a recursive procedure through which physical individuation is also acting on "its own theatre". We represent this procedure like a mapping through which (R1R2) are applied to themselves, so that: RN = (R1R2)N. We highlight the relation between this assumption and the concept of extended criticality developed by Bailly, Longo and Montévil.

Aging as alteration.

Aging is a normative biological process, and not simply a physical one. It is not accurate to define it by the fact that life has an entropic cost, and to characterize it as a pure imbalance between exergonic and endergonic reaction in metabolism (the free radical theory of aging) or finally as an imbalance between the excessive formation of reactive oxygen species and limited antioxidant defenses. In connective tissues, aging is alteration. And alteration is more than destruction or degradation. It deals with self-destruction and with the so-called molecular vicious circles of aging. In worms, in yeast, and in other organisms, aging is also opposed to longevity that counteracts this self-destruction process, as if longevity was something like a developmental constraint (delay) opposed to an evolutionary one (alteration).

Extended physics as a theoretical framework for systems biology?

In this essay we examine whether a theoretical and conceptual framework for systems biology could be built from the Bailly and Longo (2008, 2009) proposal. These authors aim to understand life as a coherent critical structure, and propose to develop an extended physical approach of evolution, as a diffusion of biomass in a space of complexity. Their attempt leads to a simple mathematical reconstruction of Gould's assumption (1989) concerning the bacterial world as a "left wall of least complexity" that we will examine. Extended physical systems are characterized by their constructive properties. Time is acting and new properties emerge by their history that can open the list of their initial properties. This conceptual and theoretical framework is nothing more than a philosophical assumption, but as such it provides a new and exciting approach concerning the evolution of life, and the transition between physics and biology.

[Epistemological views about vicious epigenetic circles due to aging]. / Considérations épistémologiques sur les cercles vicieux épigénétiques du vieillissement.

Aging is not a disease. Age changes occur in every adult animal. They take place in all species. Yet, malignant tumours and neurodegenerative diseases grow with age. Nobody dies from aging. Death results from age-associated diseases. Muscular and digestive atrophies rise with age. But should it be said that digestive atrophy leads to malnutrition, or is it the contrary? Where is the chicken and where is the egg? We are enclosed in a vicious circle. A vicious circle is not a simple cycle. It is an irreversible phenomenon that happens when a system of objects is acting on itself. Vicious circles now reach the molecular level. This paper tries to show that the destruction of elastin and of fibronectin in connective tissues produces a self destruction effect. Von Neumann showed that a model of self reproduction with the help of reproductive automata could be imagined. We attempt now to show that nature has imagined a model to produce self destruction, trough degradation products of fibronectin and of elastin. This self destruction process is neither purely stochastic, nor genetically programmed. It is an epigenetical process. It is not present in the beginning, as an a priori instruction, it emerges. We try to give here a unusual specific philosophical definition of the word "emergence".