Continua in Biological Systems

Schulz, Steffan W.; Johansson, Ingvar

doi:10.5840/monist200790434

Cited by 17 publications

(19 citation statements)

References 17 publications

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“…[24]). This is insofar problematic, as connectedness comes in degrees, which at its turn results from an underlying continuity problem [12], [17] that frequently impedes consistently distinguishing bona fide from fiat boundaries.…”

Section: Resultsmentioning

confidence: 99%

“…Biological objects are the product of evolution and exhibit a high degree of variability that constitutes a complex network of relations of similarities and differences between all objects of the enlivened nature. Accordingly, biologists have to deal with a continuum of forms and functions that spans a complex morphological property space, in which usually no two objects occupy exactly the same place [12]. This alone poses considerable conceptual problems [27], and many of the concepts used for referring to specific types of entities within this continuum are delineated by fiat (cf.…”

Section: Resultsmentioning

confidence: 99%

“…Thus, one can even talk about fiat concepts in a conceptual sense, or about perceptual, ecological, geometrical, legal, administrative, political and linguistic fiats (e.g., [7], [8], [12]). Obviously, the distinction of fiat and bona fide goes beyond the physical realm and is very general.…”

Section: Introductionmentioning

confidence: 99%

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Fiat or Bona Fide Boundary—A Matter of Granular Perspective

et al. 2012

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BackgroundDistinguishing bona fide (i.e. natural) and fiat (i.e. artificial) physical boundaries plays a key role for distinguishing natural from artificial material entities and is thus relevant to any scientific formal foundational top-level ontology, as for instance the Basic Formal Ontology (BFO). In BFO, the distinction is essential for demarcating two foundational categories of material entity: object and fiat object part. The commonly used basis for demarcating bona fide from fiat boundary refers to two criteria: (i) intrinsic qualities of the boundary bearers (i.e. spatial/physical discontinuity, qualitative heterogeneity) and (ii) mind-independent existence of the boundary. The resulting distinction of bona fide and fiat boundaries is considered to be categorial and exhaustive.Methodology/Principal FindingsBy referring to various examples from biology, we demonstrate that the hitherto used distinction of boundaries is not categorial: (i) spatial/physical discontinuity is a matter of scale and the differentiation of bona fide and fiat boundaries is thus granularity-dependent, and (ii) this differentiation is not absolute, but comes in degrees. By reducing the demarcation criteria to mind-independence and by also considering dispositions and historical relations of the bearers of boundaries, instead of only considering their spatio-structural properties, we demonstrate with various examples that spatio-structurally fiat boundaries can nevertheless be mind-independent and in this sense bona fide.Conclusions/SignificanceWe argue that the ontological status of a given boundary is perspective-dependent and that the strictly spatio-structural demarcation criteria follow a static perspective that is ignorant of causality and the dynamics of reality. Based on a distinction of several ontologically independent perspectives, we suggest different types of boundaries and corresponding material entities, including boundaries based on function (locomotion, physiology, ecology, development, reproduction) and common history (development, heredity, evolution). We argue that for each perspective one can differentiate respective bona fide from fiat boundaries.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

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Fiat or Bona Fide Boundary—A Matter of Granular Perspective

et al. 2012

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“…Contributing causal factors, (quasi)simultaneous causation, reciprocal causation, and bio-causal feedback mechanisms will be involved. In short, considering only sequential/linear causal scenarios does not do justice to biological reality, which is more interrelated and continuous (Schulz & Johansson, 2007). Desiderata for any causal account of disease includes the ability to represent this complexity.…”

Section: (A5) Instance_of(x Causally-linked Occurrent) → ∃Y Instancementioning

confidence: 99%

“…"The course of a disease is a unity of such entities that is characterized by abnormal functioning" (Schulz & Johansson, 2007), and related pathological processes causing that dysfunction. Constitution relates potentially compresent or coincident entities of disjoint categories.…”

Section: The River Flow Model Disease Definitionmentioning

confidence: 99%

Causality and the ontology of disease

Rovetto

Mizoguchi

2015

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Abstract. The goal of this paper is two-fold: first, to emphasize causality in disease ontology and knowledge representation, presenting a general and cursory discussion of causality and causal chains; and second, to clarify and develop the River Flow Model of Diseases (RFM). The RFM is an ontological account of disease, representing the causal structure of pathology. It applies general knowledge of causality using the concept of causal chains. The river analogy of disease is explained, formal descriptions are offered, and the RFM disease definition is refined by describing causal chains in terms of causal relations. The definition is updated to coincide with the actual RFM classes found in its upper-level ontology, YAMATO, which brings to light some challenges in developing both YAMATO and the RFM. The RFM is also discussed in relation to another ontological account of disease. Strategies are offered toward interoperability between these theories.

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The need for data standards in zoomorphology

Vogt

Nickel

Jenner

et al. 2013

Journal of Morphology

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eScience is a new approach to research that focuses on data mining and exploration rather than data generation or simulation. This new approach is arguably a driving force for scientific progress and requires data to be openly available, easily accessible via the Internet, and compatible with each other. eScience relies on modern standards for the reporting and documentation of data and metadata. Here, we suggest necessary components (i.e., content, concept, nomenclature, format) of such standards in the context of zoomorphology. We document the need for using data repositories to prevent data loss and how publication practice is currently changing, with the emergence of dynamic publications and the publication of digital datasets. Subsequently, we demonstrate that in zoomorphology the scientific record is still limited to published literature and that zoomorphological data are usually not accessible through data repositories. The underlying problem is that zoomorphology lacks the standards for data and metadata. As a consequence, zoomorphology cannot participate in eScience. We argue that the standardization of morphological data requires i) a standardized framework for terminologies for anatomy and ii) a formalized method of description that allows computer-parsable morphological data to be communicable, compatible, and comparable. The role of controlled vocabularies (e.g., ontologies) for developing respective terminologies and methods of description is discussed, especially in the context of data annotation and semantic enhancement of publications. Finally, we introduce the International Consortium for Zoomorphology Standards, a working group that is open to everyone and whose aim is to stimulate and synthesize dialog about standards. It is the Consortium's ultimate goal to assist the zoomorphology community in developing modern data and metadata standards, including anatomy ontologies, thereby facilitating the participation of zoomorphology in eScience.

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Continua in Biological Systems

Cited by 17 publications

References 17 publications

Fiat or Bona Fide Boundary—A Matter of Granular Perspective

Fiat or Bona Fide Boundary—A Matter of Granular Perspective

Causality and the ontology of disease

The need for data standards in zoomorphology

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