Willard van Orman Quine once said that he had a preference for a desert ontology. This was in an earlier day when concerns with logical structure and ontological simplicity reigned supreme. Ontological genocide was practiced upon whole classes of upper-level or ‘derivative’ entities in the name of elegance, and we were secure in the belief that one strayed irremediably into the realm of conceptual confusion and possible error the further one got from ontic fundamentalism. In those days, one paid more (...) attention to generic worries about possible errors than to actual errors derived from distancing oneself too far from the nitty-gritty details of actual theory, actual inferences from actual data, the actual conditions under which we posited and detected entities, calibrated and ‘burned in’ instruments, identified and rejected artifacts, debugged programs and procedures, explained the mechanisms behind regularities, judged correlations to be spurious, and in general, to the real complexities and richness of actual scientific practice. (shrink)

Discusses the ethical implications of modern technology and examines the responsibility of humanity for the fate of the world.

By linking the concepts of homology and morphological organization to evolvability, this paper attempts to (1) bridge the gap between developmental and phylogenetic approaches to homology and to (2) show that developmental constraints and natural selection are compatible and in fact complementary. I conceive of a homologue as a unit of morphological evolvability, i.e., as a part of an organism that can exhibit heritable phenotypic variation independently of the organism’s other homologues. An account of homology therefore consists in explaining how (...) an organism’s developmental constitution results in different homologues/characters as units that can evolve independently of each other. The explanans of an account of homology is developmental, yet the very explanandum is an evolutionary phenomenon: evolvability in a character-by-character fashion, which manifests itself in phylogenetic patterns as recognized by phylogenetic approaches to homology. While developmental constraints and selection have often been viewed as antagonistic forces, I argue that both are complementary as they concern different parts of the evolutionary process. Developmental constraints, conceived of as the presence of the same set of homologues across phenotypic change, pertain to how heritable variation can be generated in the first place (evolvability), while natural selection operates subsequently on the produced variation. (shrink)

Adaptive evolution is usually assumed to be directed by selective processes, development by instructive processes; evolution involves random genetic changes, development involves induced epigenetic changes. However, these distinctions are no longer unequivocal. Selection of genetic changes is a normal part of development in some organisms, and through the epigenetic system external factors can induce selectable heritable variations. Incorporating the effects of instructive processes into evolutionary thinking alters ideas about the way environmental changes lead to evolutionary change, and about the interplay (...) between genetic and epigenetic systems. (shrink)

This review paper discusses the perspective of complex biological systems as applied to inheritance and ontogeny, focusing on the continuity of genetic, epigenetic and microbiotic inheritance. The informational processuality within this continuity can be used as to exemplify the insufficiency of hierarchical concepts in grasping the complex and integrated nature of biological processes. The argument follows Bruni and Giorgi in emphasizing that while structures and substrates are organized hierarchically, communicational processes are organized heterarchically. The essay also argues the insufficiency of (...) a single, basic, i.e. genetic level of description, which is the prevalent idea of twentieth century biology, to explain all phenotypic variation. I argue that inheritance and development cannot be fully explained by some sub- or super-ordination and that such descriptions are merely heuristic tools that do not reflect the nature of such processes. (shrink)

While the field of semiotics has been active since it was started by Peirce, it appears like the last decade has been especially productive with a number of important new concepts being developed within the biosemiotics community. The novel concept of the Semiotic scaffold by Hoffmeyer is an important addition that offers insight into the hardware requirements for bio-semiosis. As any type of semiosis must be dependent upon Semiotic scaffolds, I recently argued that the process of semiosis has to be (...) divided into two separate processes of sign establishment and sign interpretation, and that misalignment between the two processes result in faulty sign interpretation and over-signification. Such faulty signs were forbidden in the sign classification system of Peirce, so I defined them as forbidden signs. Here I present an analysis of the forbidden sign categories with examples from Occult semiotics. I also show that biological semiosis offers examples of forbidden signs, where the faulty interpretation of signs may lead to decimation of whole evolutionary lines of organisms. A new concept of Evolutionary memory which is applicable to both human and biological semiosis is explained as the combination of two processes; one leading to diversity generation within semiotic scaffolds followed by a second process of decimation of faulty signs during selection in specific learning environments. The analysis suggests that forbidden signs are always used as early stages in the iterative sign establishment process during semiosis. (shrink)

Cell communication plays a key role in multicellular organisms. In developing embryos as in adult organisms, cells communicate by coordinating their differentiation through the establishment and/or renewal of a variety of cell communication channels. Under both these conditions, cells interact by either receptor signalling, surface recognition of specific cell adhesion molecules or transfer of cytoplasmic components through junctional coupling. In recent years, it has become apparent that cells may also communicate through the extracellular release of microvesicles. They may originate as (...) either exosomes from the endosomal compartment upon fusion of multivesicular bodies with the plasma membrane or be shed directly from the plasma membrane via extensions of the cell surface. Microvesicles may disperse over long distances through body fluids and deliver their molecular cargo onto a variety of target cells. As a general rule, the metabolic fate of these cells is determined by the molecular nature of the vesicular cargo, while targeting itself depends on the affinity of the molecules expressed on the enclosing membrane. In this paper, we will be arguing that intercellular vesicular transfer is substantially different from other types of cell communication, allowing cells and molecules to interact on varying levels. Cells interacting via ligand signalling owe their specificity to the steric coupling with cognate receptor molecules. As such, it is a pure molecular process that affects target cells only upon integration into their responding repertoire. In this relationship, coupled cells are reciprocally adapted to each other through the selection of their respective signalling capacities, following exploration of their receptor specificity. Interaction by intercellular vesicles realizes a substantially different type of cell communication. Vesicular traffic allows donor cells to carry out a horizontal type of gene transfer and target this information over long distances via independently controlled mechanisms. Because of this independence, cells interacting via vesicular traffic are not expected to adapt their signalling correspondences, but to control instead the efficiency of their cargo delivery irrespective of the receptor repertoire expressed by the target tissue. In this paper, the multifaceted functions of the intercellular vesicular traffic will be discussed in a multilevel biosemiotic perspective with the aim of unravelling the cellular mechanisms devised by nature to accomplish communication. (shrink)

What changes when an evolutionary transition in individuality takes place? Many different answers have been given, in respect of different cases of actual transition, but some have suggested a general answer: that a major transition is a change in the extent to which selection acts at one hierarchical level rather than another. The current paper evaluates some different ways to develop this general answer as a way to characterise the property ‘evolutionary individuality’; and offers a justification of the option taken (...) in Clarke :413–435, 2013)—to define evolutionary individuality in terms of an object’s capacity to undergo selection at its own level. In addition, I suggest a method by which the property can be measured and argue that a problem which is often considered to be fatal to that method—the problem of ‘cross-level by-products’—can be avoided. (shrink)

Genetic interventions, which include transgenic engineering, gene editing, and other forms of genome modification aimed at altering the information “in” the genetic code, are rapidly increasing in power and scale. Biosemiotics offers unique tools for understanding the nature, risks, scope, and prospects of such technologies, though few in the community have turned their attention specifically in this direction. Bruni is an important exception. In this paper, I examine how we frame the concept of “side effects” that result from genetic interventions (...) and how the concept stands up to current perspectives of the role of organism activity in development. I propose that once the role of living systems in constructing and modifying the informational value of their various developmental resources is taken into account, the concept of a “side effect” will need to be significantly revised. Far from merely a disturbance brought about in a senseless albeit complex system, a biosemiotic view would take “side effects” as at least sometimes the organism’s active re-organization in order to accommodate or make use of novelty. This insight is nascent in the work of developmental plasticity and niche construction theory, but it is brought into sharper focus by the explicitly interpretive perspective offered by biosemiotics. Understanding the “side effects” of genetic interventions depends in part on being able to articulate when and where unexpected consequences are a result of semiotic activity at various levels within the system. While a semiotic interpretation of “side effects” puts into question the naive attitude that would see all unintended side effects as indications of disturbance in system functionality, it certainly does not imply that such side effects are of no concern for the viability of the organisms in the system. As we shall see, the fact that such interventions do not respect the translation of information that occurs in multi-level biological systems ensures that disruption is still likely. But it does unprivilege the human agent as the sole generator of meaning and information in the products of biotechnology, with important consequences on how we understand our relationship with other species. (shrink)

Between 1940 and 1970 pioneers in the new field of cell biology discovered the operative parts of cells and their contributions to cell life. They offered mechanistic accounts that explained cellular phenomena by identifying the relevant parts of cells, the biochemical operations they performed, and the way in which these parts and operations were organised to accomplish important functions. Cell biology was a revolutionary science but in this book it also provides fuel for yet another revolution, one that focuses on (...) the very conception of science itself. Laws have traditionally been regarded as the primary vehicle of explanation, but in the emerging philosophy of science it is mechanisms that do the explanatory work. Bechtel emphasises how mechanisms were discovered, focusing especially on the way in which new instruments made these inquiries possible. He also describes how new journals and societies provided institutional structure to this new enterprise. (shrink)

Between 1940 and 1970 pioneers in the new field of cell biology discovered the operative parts of cells and their contributions to cell life. They offered mechanistic accounts that explained cellular phenomena by identifying the relevant parts of cells, the biochemical operations they performed, and the way in which these parts and operations were organised to accomplish important functions. Cell biology was a revolutionary science but in this book it also provides fuel for yet another revolution, one that focuses on (...) the very conception of science itself. Laws have traditionally been regarded as the primary vehicle of explanation, but in the emerging philosophy of science it is mechanisms that do the explanatory work. Bechtel emphasises how mechanisms were discovered, focusing especially on the way in which new instruments made these inquiries possible. He also describes how new journals and societies provided institutional structure to this new enterprise. (shrink)