This paper compares the two known logical forms of hierarchy, both of which have been used in models of natural phenomena, including the biological. I contrast their general properties, internal formal relations, modes of growth (emergence) in applications to the natural world, criteria for applying them, the complexities that they embody, their dynamical relations in applied models, and their informational relations and semiotic aspects.

This article addresses the problem of emergence through a distinction, often neglected in the literature, between two different aspects of this issue: (1) the theoretical problem of providing modelizations able to explain the expression of emergent properties; (2) the epistemological problem of warranting the scientific value of the emergentist descriptions of nature. This paper considers this double issue with regard to the biological domain, and proposes a double solution (theoretical and epistemological) originally developed in early studies on self-organization. The underlying (...) hypothesis is that this solution offers the current biological emergentism the opportunity of developing a coherent structure: matching consistently the theoretical and the epistemological frames of the research, that is, coupling the emergentist conception of life with an emergentist conception of science. (shrink)

The concept of downward causation is frequently used in an explanatory capacity in biology to account for certain regularities and processes. Some philosophers, however, argue that downward causation is metaphysically incoherent, providing three main objections. Underlying these objections is the assumption that entities are connected by compositional hierarchies of levels of organization. In this paper, I introduce the notions of weak and strong compositional relations using examples from evolutionary developmental biology. I argue that downward causation becomes unproblematic if we use (...) features of interventionist theories of causation to explain the causal relations between levels. I show that an interventionist account of downward causation successfully responds to the three central objections to downward causation in the philosophical literature and I clarify the explanatory usefulness of the concept in biology. As such, this paper provides an epistemic solution to demystify downward causation in the context of scientific practice. The solution proposed is compatible with how biologists seem to use a concept of downward causation fruitfully in their work. (shrink)

The author argues that the reductionist illusions of the Modern Synthesis, which Noble criticizes in his target article, are to a large extent resulting from a mere syntactical notion of biological information, neglecting the pragmatic and semantic dimension of information. Although the syntactical notion, introduced by Shannon, has been applied with much success in information theory and computer technologies, it is too narrow to understand biological reality. Biosemiotics can help to clarify the problems identified by Noble, and offers a more (...) adequate biological information concept, which not only may help to overcome these problems in the life sciences, but may also serve to integrate natural-scientific and humanities approaches to life. (shrink)

A novel non-classical mereological concept built up by blending the Metaphysics of Xavier Zubiri and the Quantum Theory of Atoms in Molecules of R. F. W. Bader is proposed. It is argued that this philosophical concept is necessary to properly account for what happens in a chemical reaction. From the topology of the gradient of the laplacian of the electronic charge density, \\) within the QTAIM framework, different “atomic graphs” are found for each atom depending on the molecular context, reflecting (...) how the whole molecule affects each atom. In this way, the whole molecular system imposes certain geometry onto each atom, and every atom exhibits different ontological modality. On the Metaphysical side, for X. Zubiri real things are system of different notes. The physical essence is the subsystem of essential notes with a coherence unity. Every note is grounded on the essence. The unity of the system is present somehow in every note-of beforehand, and every essential note-of turns towards the other. The essence determines the position of each note within the system, and hence is the grounding for modality of the notes. By conflating both “theories” and taking the atoms as essential notes, we propose the concept of “Molecule in atoms-of” or “atoms-of in Molecules”. Within the course of a chemical reaction the atoms-of modified their “of” as required by the new molecular unity being formed, and eventually change their modality. The validity to the Zubiri’s statements, is attained by evaluating necessity and possibility in a set-up of finite accessible “possible worlds”. (shrink)

The term ‘information’ is used extensively in biology, cognitive science and the philosophy of consciousness in relation to the concepts of ‘meaning’ and ‘causation’. While ‘information’ is a term that serves a useful purpose in specific disciplines, there is much to the concept that is problematic. Part 1 is a critique of the stance that information is an independently existing entity. On this view, and in biological contexts, systems transmit, acquire, assimilate, decode and manipulate it, and in so doing, generate (...) meaning. I provide a detailed proposal in Part 2 that supports the claim that it is the dynamic form of a system that qualifies the informational nature of meaningful interactive engagement, that is, that information is dependent on dynamic form rather than that it exists independently. In Part 3, I reflect on the importance of the distinction between the independent and dependent stances by looking specifically at the implications for how we might better interpret causation and emergence. (shrink)

This paper proposes an integrated-structure notion of interlevel emergence, from a dynamic relational ontological perspective. First, I will argue that only the individualist essentialism of atomistic metaphysics can block the possibility of interlevel emergence. Then I will show that we can make sense of emergence by recognizing the formation of structures of transformative and interdependent causal relations in the generation and development of a particular class of mereological complexes called integrated systems. Finally, I shall argue that even though the emergent (...) structural attributes of such systems are not micro-determined nor micro-reducible, they can still be accounted for by an interlevel integrative neo-mechanistic form of explanation. (shrink)

In the course of the 20th century the so-called Modern Synthesis of Neo-Darwinism has become the dominant paradigm in modern biology. First, it is explained how and why Darwin’s broad definition of evolution, in which the environment plays an important role, was narrowed down by Neo-Darwinism to a radical gene-centric view. Next, the paradigm shift taking place today in ‘postgenomic’ evolutionary biology and genetics is discussed. It is argued that this shift opens the way to a more humane conception of (...) evolution, more in line with Darwin’s view. Finally, I will discuss some of the implications of this paradigm shift for human self-reflection, taking The Music of Life. Biology Beyond Genes of systems biologist Denis Noble as a starting point. (shrink)

Helmuth Plessner’s Levels of Organic Life and the Human [Die Stufen des Organischen und der Mensch, 1928] is one of the founding texts of twentieth century philosophical anthropology (understood as philosophical reflection on the fundamental characteristics of the human lifeform). It is argued that Plessner’s work demonstrates the fundamental indispensability of the qualitative humanities vis-à-vis the natural-scientific study of man. Plessner’s non-reductionist, emergentist naturalism allots complementary roles to the causal and functional investigations of the life sciences and the phenomenological and (...) hermeneutic interpretation of the phenomenon of life in its successive levels and stages. Within this context, human agency can be understood as a higher-order property of organic life, which act by the selective activation of lower-level psychophysical powers. Plessner’s three ‘anthropological laws’ are used to situate the notion of practical self-understanding in between two extremes: deterministic views that deny human freedom and responsibility and views that ascribe an unrealistic amount of autonomy to human beings. (shrink)

This paper first queries what type of concept of emergence, if any, could be connected with the different chemical activities subsumed under the label ‘quantum chemistry’. In line with Roald Hoffmann, we propose a ‘rotation to research laboratory’ in order to point out how practitioners hold a molecular whole, its parts, and the surroundings together within their various methods when exploring chemical transformation. We then identify some requisite contents that a concept of emergence must incorporate in order to be coherent (...) from the standpoint of the scientific practices involved. In this respect, we finally propose a relational form of emergence which pays attention to the constitutive role of the modes of intervention and to the co-definition of the levels of organization. No metaphysical distinction between the higher and basic levels of organization is supposed, but only a plurality of modes of access. Moreover, these modes of access are not construed as mere ways of revealing intrinsic patterns of organization but, on the contrary, are considered to be active elements on which the constitution of those patterns depends. What is at stake in this paper is therefore not an ontological form of emergence but an agnostic one which fits what chemists do in their daily work. (shrink)

Helmuth Plessner’s Levels of Organic Life and the Human [Die Stufen des Organischen und der Mensch, 1928] is one of the founding texts of twentieth century philosophical anthropology. It is argued that Plessner’s work demonstrates the fundamental indispensability of the qualitative humanities vis-à-vis the natural-scientific study of man. Plessner’s non-reductionist, emergentist naturalism allots complementary roles to the causal and functional investigations of the life sciences and the phenomenological and hermeneutic interpretation of the phenomenon of life in its successive levels and (...) stages. Within this context, human agency can be understood as a higher-order property of organic life, which act by the selective activation of lower-level psychophysical powers. Plessner’s three ‘anthropological laws’ are used to situate the notion of practical self-understanding in between two extremes: deterministic views that deny human freedom and responsibility and views that ascribe an unrealistic amount of autonomy to human beings. (shrink)