Universality, complexity and the praxis of biology: Two case studies

Tree size distribution as the stationary limit of an evolutionary master equation

The diameter distribution of a given species of deciduous trees is well approximated by a Gamma distribution. Here we give new experimental evidence for this conjecture by analyzing deciduous tree size data in mature semi-natural forest and ancient, traditionally managed wood-pasture from Central Europe. These distribution functions collapse on a universal shape if the tree sizes are normalized to the mean value in the considered sample. A new evolutionary master equation is used to model the observed distribution. The model incorporates four ecological processes: tree growth, mortality, recruitment, and diversification. Utilizing simple and realistic kernel functions describing the first three, along with an assumed multiplicative dilution due to diversification, the stationary solution of the master equation yields the experimentally observed Gamma distribution. The model as it is formulated allows an analytically compact solution and has only two fitting parameters whose values are consistent with the experimental data related to these processes. We found that the equilibrium size distribution of tree species with different ecology, originating from two contrastingly different semi-natural ecosystem types can be accurately described by a single dynamical mean-field model.

Clinical Phenotypes of Cardiovascular and Heart Failure Diseases Can Be Reversed? The Holistic Principle of Systems Biology in Multifaceted Heart Diseases

Recent advances in cardiology and biological sciences have improved quality of life in patients with complex cardiovascular diseases (CVDs) or heart failure (HF). Regardless of medical progress, complex cardiac diseases continue to have a prolonged clinical course with high morbidity and mortality. Interventional coronary techniques together with drug therapy improve quality and future prospects of life, but do not reverse the course of the atherosclerotic process that remains relentlessly progressive. The probability of CVDs and HF phenotypes to reverse can be supported by the advances made on the medical holistic principle of systems biology (SB) and on artificial intelligence (AI). Studies on clinical phenotypes reversal should be based on the research performed in large populations of patients following gathering and analyzing large amounts of relative data that embrace the concept of complexity. To decipher the complexity conundrum, a multiomics approach is needed with network analysis of the biological data. Only by understanding the complexity of chronic heart diseases and explaining the interrelationship between different interconnected biological networks can the probability for clinical phenotypes reversal be increased.

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 R_N = (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.

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: R_N = (R₁R₂)^N. We highlight the relation between this assumption and the concept of extended criticality developed by Bailly, Longo and Montévil.

Can functionality in evolving networks be explained reductively?

Philosophers of biology disagree about an adequate explication of the concept of function. Instead of perpetuating the debate on the level of in principle-arguments, this paper aims first at reconstructing functional talk in the biological research papers of Marom and Braun, which focus on two different kinds of evolving networks, and in discussing the ontological consequences which the authors draw from their results. Marom investigates evolving neural networks controlling Braitenberg vehicles. Braun observes the evolutionary rearrangement or "rewiring" of the genetic network of genetically modified yeast on a short time scale. In both cases, the parameters under investigation are defined in functional terms. However, both authors report striking differences in the structures that realize one and the same function, as well as striking differences in the function of identical structures. From this, they construct an argument against reductionism. The second aim of my paper is an inquiry into the epistemic legitimacy of this conclusion. This requires addressing critically several concepts on which Marom and Braun's argument is built.

Can mechanistic explanation be reconciled with scale-free constitution and dynamics?

This paper considers two objections to explanations that appeal to mechanisms to explain biological phenomena. Marom argues that the time-scale on which many phenomena occur is scale-free. There is also reason to suspect that the network of interacting entities is scale-free. The result is that mechanisms do not have well-delineated boundaries in nature. I argue that bounded mechanisms should be viewed as entities scientists posit in advancing scientific hypotheses. In positing such entities, scientists idealize. Such idealizations can be highly productive in developing and improving scientific explanations even if the hypothesized mechanisms never precisely correspond to bounded entities in nature. Mechanistic explanations can be reconciled with scale-free constitution and dynamics even if mechanisms as bounded entities don't exist.

Can biological complexity be reverse engineered?

Concerns with the use of engineering approaches in biology have recently been raised. I examine two related challenges to biological research that I call the synchronic and diachronic underdetermination problem. The former refers to challenges associated with the inference of design principles underlying system capacities when the synchronic relations between lower-level processes and higher-level systems capacities are degenerate (many-to-many). The diachronic underdetermination problem regards the problem of reverse engineering a system where the non-linear relations between system capacities and lower-level mechanisms are changing over time. Braun and Marom argue that recent insights to biological complexity leave the aim of reverse engineering hopeless - in principle as well as in practice. While I support their call for systemic approaches to capture the dynamic nature of living systems, I take issue with the conflation of reverse engineering with naïve reductionism. I clarify how the notion of design principles can be more broadly conceived and argue that reverse engineering is compatible with a dynamic view of organisms. It may even help to facilitate an integrated account that bridges the gap between mechanistic and systems approaches.