Björn Quast

Publications (4)13.56 Total impact

• Article: Fiat or Bona Fide Boundary—A Matter of Granular Perspective

  Lars Vogt, Peter Grobe, Björn Quast, Thomas Bartolomaeus
  [show abstract] [hide abstract]
  ABSTRACT: Background: Distinguishing 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 Findings: By 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/Significance: We 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.
  PLoS ONE 12/2012; 7(12):e48603. · 4.09 Impact Factor
• Article: Nephridial development and body cavity formation in Artemia salina (Crustacea: Branchiopoda): no evidence for any transitory coelom

  Thomas Bartolomaeus, Björn Quast, Markus Koch
  [show abstract] [hide abstract]
  ABSTRACT: The Ecdysozoa-hypothesis on the origin of arthropods questions the homology of segmentation in arthropods, onychophorans, and annelids. The implication of convergent gain of metamery in these groups seems to conflict particularly with the correspondence in the development of serial coelomic cavities and metanephridia. Ultrastructural studies of the mesoderm development in Onychophora revealed that main correspondence with the state in annelids concerns the involvement of epithelial lining cells of the embryonic coelomic cavities in the formation of the visceral and somatic musculature. The significance of this correspondence, however, remained unclear as comparable data on the state in arthropods were still missing. Developmental studies on selected representatives covering all major arthropod subgroups aim to fill in this gap. Data were raised by a combination of transmission electron microscopy and fluorescent stainings of the muscular system and nuclei for the anostracan crustacean Artemia salina. In this species, putative transitory coelomic cavities proved to be absent in all trunk segments. In the second antennal and second maxillary segments small, compact nephridial anlagen develop into a sacculus and excretory duct. The sacculus originates from the terminal cells of the nephridial duct, which is formed in advance. The lumen of the sacculus is inconspicuous in its earliest functional stage and later enlarges to a bulb; it accordingly represents no remnant of any primarily large coelomic cavity. The muscular system is entirely formed prior to and independent of coelomic or nephridial anlagen. Visceral and somatic mesoderm already separate in the caudal body region. Transitory segmental clusters of mesodermal cells are composed of somatic cells only and accordingly represent no “somites”. Our observations overall do not provide any support for the homology of coelomic cavities in annelids and arthropods.
  Zeitschrift für Morphologie der Tiere 04/2012; 128(3):247-262. · 1.28 Impact Factor
• Source

  Available from: dx.plos.org

  Article: Accommodating ontologies to biological reality--top-level categories of cumulative-constitutively organized material entities.

  Lars Vogt, Peter Grobe, Björn Quast, Thomas Bartolomaeus
  [show abstract] [hide abstract]
  ABSTRACT: The Basic Formal Ontology (BFO) is a top-level formal foundational ontology for the biomedical domain. It has been developed with the purpose to serve as an ontologically consistent template for top-level categories of application oriented and domain reference ontologies within the Open Biological and Biomedical Ontologies Foundry (OBO). BFO is important for enabling OBO ontologies to facilitate in reliably communicating and managing data and metadata within and across biomedical databases. Following its intended single inheritance policy, BFO's three top-level categories of material entity (i.e. 'object', 'fiat object part', 'object aggregate') must be exhaustive and mutually disjoint. We have shown elsewhere that for accommodating all types of constitutively organized material entities, BFO must be extended by additional categories of material entity. Unfortunately, most biomedical material entities are cumulative-constitutively organized. We show that even the extended BFO does not exhaustively cover cumulative-constitutively organized material entities. We provide examples from biology and everyday life that demonstrate the necessity for 'portion of matter' as another material building block. This implies the necessity for further extending BFO by 'portion of matter' as well as three additional categories that possess portions of matter as aggregate components. These extensions are necessary if the basic assumption that all parts that share the same granularity level exhaustively sum to the whole should also apply to cumulative-constitutively organized material entities. By suggesting a notion of granular representation we provide a way to maintain the single inheritance principle when dealing with cumulative-constitutively organized material entities. We suggest to extend BFO to incorporate additional categories of material entity and to rearrange its top-level material entity taxonomy. With these additions and the notion of granular representation, BFO would exhaustively cover all top-level types of material entities that application oriented ontologies may use as templates, while still maintaining the single inheritance principle.
  PLoS ONE 01/2012; 7(1):e30004. · 4.09 Impact Factor
• Source

  Available from: Lars Vogt

  Article: Top-level categories of constitutively organized material entities--suggestions for a formal top-level ontology.

  Lars Vogt, Peter Grobe, Björn Quast, Thomas Bartolomaeus
  [show abstract] [hide abstract]
  ABSTRACT: Application oriented ontologies are important for reliably communicating and managing data in databases. Unfortunately, they often differ in the definitions they use and thus do not live up to their potential. This problem can be reduced when using a standardized and ontologically consistent template for the top-level categories from a top-level formal foundational ontology. This would support ontological consistency within application oriented ontologies and compatibility between them. The Basic Formal Ontology (BFO) is such a foundational ontology for the biomedical domain that has been developed following the single inheritance policy. It provides the top-level template within the Open Biological and Biomedical Ontologies Foundry. If it wants to live up to its expected role, its three top-level categories of material entity (i.e., 'object', 'fiat object part', 'object aggregate') must be exhaustive, i.e. every concrete material entity must instantiate exactly one of them. By systematically evaluating all possible basic configurations of material building blocks we show that BFO's top-level categories of material entity are not exhaustive. We provide examples from biology and everyday life that demonstrate the necessity for two additional categories: 'fiat object part aggregate' and 'object with fiat object part aggregate'. By distinguishing topological coherence, topological adherence, and metric proximity we furthermore provide a differentiation of clusters and groups as two distinct subcategories for each of the three categories of material entity aggregates, resulting in six additional subcategories of material entity. We suggest extending BFO to incorporate two additional categories of material entity as well as two subcategories for each of the three categories of material entity aggregates. With these additions, BFO would exhaustively cover all top-level types of material entity that application oriented ontologies may use as templates. Our result, however, depends on the premise that all material entities are organized according to a constitutive granularity.
  PLoS ONE 01/2011; 6(4):e18794. · 4.09 Impact Factor