Towards a Model of Life and Cognition

What should be the ontology of the world such that life and cognition are possible? In this essay, I undertake to outline an alternative ontological foundation which makes biological and cognitive phenomena possible. The foundation is built by defining a model, which is presented in the form of a description of a hypothetical but a logically possible world with a defined ontological base. Biology rests today on quite a few not so well connected foundations: molecular biology based on the genetic dogma; evolutionary biology based on neo-Darwinian model; ecology based on systems view; developmental biology by morphogenetic models; connectionist models for neurophysiology and cognitive biology; pervasive teleonomic explanations for the goal-directed behavior across the discipline; etc. Can there be an underlying connecting theme or a model which could make these seemingly disparate domains interconnected? I shall atempt to answer this question. By following the semantic view of scientific theories, I tend to believe that the models employed by the present physical sciences are not rich enough to capture biological (and some of the non-biological) systems. A richer theory that could capture biological reality could also capture physical and chemical phenomena as limiting cases, but not vice versa

Physical Properties of Biological Entities: An Introduction to the Ontology of Physics for Biology

As biomedical investigators strive to integrate data and analyses across spatiotemporal scales and biomedical domains, they have recognized the benefits of formalizing languages and terminologies via computational ontologies. Although ontologies for biological entities—molecules, cells, organs—are well-established, there are no principled ontologies of physical properties—energies, volumes, flow rates—of those entities. In this paper, we introduce the Ontology of Physics for Biology (OPB), a reference ontology of classical physics designed for annotating biophysical content of growing repositories of biomedical datasets and analytical models. The OPB's semantic framework, traceable to James Clerk Maxwell, encompasses modern theories of system dynamics and thermodynamics, and is implemented as a computational ontology that references available upper ontologies. In this paper we focus on the OPB classes that are designed for annotating physical properties encoded in biomedical datasets and computational models, and we discuss how the OPB framework will facilitate biomedical knowledge integration

Against “revolution” and “evolution”

Those standard historiographic themes of “evolution” and “revolution” need replacing. They perpetuate mid-Victorian scientists’ history of science. Historians’ history of science does well to take in the long run from the Greek and Hebrew heritages on, and to work at avoiding misleading anachronism and teleology. As an alternative to the usual “evo-revo” themes, a historiography of origins and species, of cosmologies (including microcosmogonies and macrocosmogonies) and ontologies, is developed here. The advantages of such a historiography are illustrated by looking briefly at a number of transitions the transition from Greek and Hebrew doctrines to their integrations by medieval authors; the transition from the Platonist, Aristotelian, Christian Aquinas to the Newtonian Buffon and to the no less Newtonian Lamarck; the departures the early Darwin made away from Lamarck’s and from Lyell’s views. Issues concerning historical thinking about nature, concerning essentialism and concerning classification are addressed in an attempt to challenge customary stereotypes. Questions about originality and influence are raised, especially concerning Darwin’s “tree of life” scheme. The broader historiography of Darwinian science as a social ideology, and as a “worldview,” is examined and the scope for revisions emphasised. Throughout, graduate students are encouraged to see this topic area not as worked out, but as full of opportunities for fresh contributions

Delegated causality of complex systems

A notion of delegated causality is introduced here. This subtle kind of causality is dual to interventional causality. Delegated causality elucidates the causal role of dynamical systems at the “edge of chaos”, explicates evident cases of downward causation, and relates emergent phenomena to Gödel’s incompleteness theorem. Apparently rich implications are noticed in biology and Chinese philosophy. The perspective of delegated causality supports cognitive interpretations of self-organization and evolution

The Case for Dynamic Models of Learners' Ontologies in Physics

In a series of well-known papers, Chi and Slotta (Chi, 1992; Chi & Slotta, 1993; Chi, Slotta & de Leeuw, 1994; Slotta, Chi & Joram, 1995; Chi, 2005; Slotta & Chi, 2006) have contended that a reason for students' difficulties in learning physics is that they think about concepts as things rather than as processes, and that there is a significant barrier between these two ontological categories. We contest this view, arguing that expert and novice reasoning often and productively traverses ontological categories. We cite examples from everyday, classroom, and professional contexts to illustrate this. We agree with Chi and Slotta that instruction should attend to learners' ontologies; but we find these ontologies are better understood as dynamic and context-dependent, rather than as static constraints. To promote one ontological description in physics instruction, as suggested by Slotta and Chi, could undermine novices' access to productive cognitive resources they bring to their studies and inhibit their transition to the dynamic ontological flexibility required of experts.Comment: The Journal of the Learning Sciences (In Press

Quine’s ideological debacle

In two papers in the mid-seventies, Quine has discussed an ontological deba-cle, the reduction of ontology to an ontology of pure sets only. This debacle, which weakened Quine’s interest in ontology, is the natural outcome of on-tological relativity, or, more precisely, the proxy-function argument. It is ex-plained how Quine unavoidably came to this conclusion. Moreover, it is ar-gued that the result is even more damaging for Quine’s philosophy than has hitherto been assumed. It is shown that in addition to an ontological debacle, there is an ideological debacle, reducing the ideology (lexicon) of science to the ideology of set theory. The ideological debacle results from applying ex-tensional substitution of predicates within a scientific theory that is reinter-preted by means of proxy-functions to a theory with a set-theoretic ontology. Though Quine has recognized the possibility of an ideological debacle, his rebuttal is unconvincing. As a result, his tenet of extensionalism is under heavy pressure