Ecologically responsible policies are concerned only in part with pollution and resource depletion. There are deeper concerns which touch upon principles of diversity, complexity, autonomy, decentralization, symbiosis, egalitarianism, and classlessness.

Biological evolution is a complex blend of ever changing structural stability, variability and emergence of new phe- notypes, niches, ecosystems. We wish to argue that the evo- lution of life marks the end of a physics world view of law entailed dynamics. Our considerations depend upon dis- cussing the variability of the very ”contexts of life”: the in- teractions between organisms, biological niches and ecosys- tems. These are ever changing, intrinsically indeterminate and even unprestatable: we do not know ahead of (...) time the ”niches” which constitute the boundary conditions on selec- tion. More generally, by the mathematical unprestatability of the ”phase space”, no laws of mo- tion can be formulated for evolution. We call this radical emergence, from life to life. The purpose of this paper is the integration of variation and diversity in a sound concep- tual frame and situate unpredictability at a novel theoretical level, that of the very phase space. Our argument will be carried on in close comparisons with physics and the mathematical constructions of phase spaces in that discipline. The role of symmetries as invariant preserving transformations will allow us to under- stand the nature of physical phase spaces and to stress the differences required for a sound biological theoretizing. In this frame, we discuss the novel notion of ”enablement”. Life lives in a web of enablement and radical emergence. This will restrict causal analyses to differential cases. Mutations or other causal differ- ences will allow us to stress that ”non conservation princi- ples” are at the core of evolution, in contrast to physical dynamics, largely based on conservation principles as sym- metries. Critical transitions, the main locus of symmetry changes in physics, will be discussed, and lead to ”extended criticality” as a conceptual frame for a better understanding of the living state of matter. (shrink)

Forty-two years ago, Capra published “The Tao of Physics” (Capra, 1975). In this book (page 17) he writes: “The exploration of the atomic and subatomic world in the twentieth century has …. necessitated a radical revision of many of our basic concepts” and that, unlike ‘classical’ physics, the sub-atomic and quantum “modern physics” shows resonances with Eastern thoughts and “leads us to a view of the world which is very similar to the views held by mystics of all ages and (...) traditions.“ This article stresses an analogous situation in biology with respect to a new theoretical approach for studying living systems, Integral Biomathics (IB), which also exhibits some resonances with Eastern thought. Stepping on earlier research in cybernetics1 and theoretical biology,2 IB has been developed since 2011 by over 100 scientists from a number of disciplines who have been exploring a substantial set of theoretical frameworks. From that effort, the need for a robust core model utilizing advanced mathematics and computation adequate for understanding the behavior of organisms as dynamic wholes was identified. At this end, the authors of this article have proposed WLIMES (Ehresmann and Simeonov, 2012), a formal theory for modeling living systems integrating both the Memory Evolutive Systems (Ehresmann and Vanbremeersch, 2007) and the Wandering Logic Intelligence (Simeonov, 2002b). Its principles will be recalled here with respect to their resonances to Eastern thought. (shrink)

I propose a T‐cell receptor (TcR)‐based mechanism by which immunity mediates both “genetic self” and “microbial self” thereby, connecting microbiome disease with autoimmunity. The hypothesis is based on simple principles. First, TcR are selected to avoid strong cross‐reactivity with “self,” resulting in selection for a TcR repertoire mimicking “genetic self.” Second, evolution has selected for a “microbial self” that mimics “genetic self” so as to share tolerance. In consequence, our TcR repertoire also mimics microbiome antigenicity, providing a novel mechanism for (...) modulating tolerance to it. Also, the microbiome mimics the TcR repertoire, acting as a secondary immune system. I call this TcR‐microbiome mimicry “holoimmunity” to denote immune tolerance to the “holobiont self.” Logically, microbiome‐host mimicry means that autoimmunity directed at host antigens will also attack components of the microbiome, and conversely, an immunological attack on the microbiome may cross‐react with host antigens producing “holoautoimmunity.”. (shrink)

This is one of the first books in a new series that will publish the very best work in the philosophy of biology. The series will be non-sectarian in character, will extend across the broadest range of topics, and will be genuinely interdisciplinary. The Immune Self is a critical study of immunology from its origins at the end of the nineteenth century to its contemporary formulation. The book offers the first extended philosophical critique of immunology, in which the function of (...) the term 'self' that underlies the structure of current immune theory is analysed. However, this analysis is carefully integrated into a broad survey of the major scientific developments in immunology, a discussion of their historical context, and a review of the conceptual arguments that have moulded this sophisticated modern science. (shrink)

Functional language is ubiquitous in ecology, mainly in the researches about biodiversity and ecosystem function. However, it has not been adequately investigated by ecologists or philosophers of ecology. In the contemporary philosophy of ecology we can recognize a kind of implicit consensus about this issue: while the etiological approaches cannot offer a good concept of function in ecology, Cummins’ systemic approach can. Here we propose to go beyond this implicit consensus, because we think these approaches are not adequate for ecology. (...) We argue that a sound epistemological framework to function in ecology is to be found in organizational approaches. In this line, we define function in ecology as a precise effect of a given constraint on the ecosystem flow of matter and energy performed by a given item of biodiversity, within a closure of constraints. We elaborate on this definition by developing a case study of a bromeliad ecosystem. (shrink)

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. (shrink)

This is one of the first books in a new series that will publish the very best work in the philosophy of biology. The series will be non-sectarian in character, will extend across the broadest range of topics, and will be genuinely interdisciplinary. The Immune Self is a critical study of immunology from its origins at the end of the nineteenth century to its contemporary formulation. The book offers the first extended philosophical critique of immunology, in which the function of (...) the term 'self' that underlies the structure of current immune theory is analysed. However, this analysis is carefully integrated into a broad survey of the major scientific developments in immunology, a discussion of their historical context, and a review of the conceptual arguments that have moulded this sophisticated modern science. (shrink)

Context: Immunity includes cognitive concepts: the organism is thought to specifically recognize foreign materials and develop a memory of these encounters. Vaccines are thought to work by enhancing this immunological memory. Lymphocytes are key cells and specific antibodies are key molecules in immune recognition. Antibodies are blood proteins called “immunoglobulins.” Spontaneously formed immunoglobulins are seen as “natural” antibodies to dietary components and commensal bacteria. Immune cognition is used simply as a didactic metaphor. Problem: Do the cognitive aspects of immunology stem (...) from the activities of cells and molecules, or are they ascribed by the immunologist operating as a human observer? (1) An immense variety of immunoglobulins may bind to the same antigen with different binding energies. It is the immunologist who arbitrates the boundary between those that are specific (and declared antibodies) and those that are not. Specific antibodies serve as functional labels pasted onto natural immunoglobulins, as if they were recognizing elements. Is this “arbitration” the true cognitive event ascribed to immunoglobulins and lymphocytes? (2) A major impasse exists between progress in experimental immunology and its translation into clinical results. A proper understanding of immunological activity demands a wider view of an organism’s biology and, also, of the interference of human observers in delineating experimental realities, such as the specificity of immune recognition. Maturana’s biology of cognition and language provides one such approach. Method: Use of Maturana’s biology of cognition and language concepts to describe immunological activity. Results: A whole new understanding of immunological activity is suggested. Implications: A major change in the way of seeing is proposed that may eventually help the translation of this knowledge into clinical results. Furthermore, the immune system may also become a proper model for cognitive analyses. (shrink)